Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T20891 | Target Info | |||
| Target Name | Phosphoinositide dependent protein kinase-1 (PDPK1) | ||||
| Synonyms | PDK1; HPDK1; 3-phosphoinositide-dependent protein kinase 1; 3-Phosphoinositide-dependent kinase-1; 3'-phosphoinositide dependent kinase 1 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | PDPK1 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine triphosphate | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the PIF-Pocket | PDB:5LVO | ||||
| Method | X-ray diffraction | Resolution | 1.09 Å | Mutation | Yes | [1] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSP 232 ESKQARANFV243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR 283 AGNEGLIFAK293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY 333 GPLKAHPFFE343 SVTWENLHQQ353 TPPKLT
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LEU88
3.009
GLY89
2.407
GLU90
2.837
GLY91
2.767
SER92
1.945
PHE93
4.090
SER94
1.823
THR95
4.911
VAL96
2.726
ALA109
2.982
LYS111
2.180
GLU130
4.976
VAL143
2.632
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Adenine | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Adenine Bound to the ATP-Binding Site | PDB:5LVM | ||||
| Method | X-ray diffraction | Resolution | 1.26 Å | Mutation | Yes | [1] |
| PDB Sequence |
KKRPEDFKFG
85 KILGEGSFST95 VVLARELATS105 REYAIKILEK115 RHIIKENKVP125 YVTRERDVMS 135 RLDHPFFVKL145 YFTFQDDEKL155 YFGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLSPESK 235 QARANFVGTA246 QYVSPELLTE256 KSACKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EGLIFAKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
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| Ligand Name: Adenosine | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Adenosine Bound to the ATP-Binding Site | PDB:5LVN | ||||
| Method | X-ray diffraction | Resolution | 1.38 Å | Mutation | Yes | [1] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQARANFVGT245 AQYVSPELLT255 EKSACKSSDL265 WALGCIIYQL275 VAGLPPFRAG 285 NEGLIFAKII295 KLEYDFPEKF305 FPKARDLVEK315 LLVLDATKRL325 GCEEMEGYGP 335 LKAHPFFESV345 TWENLHQQTP355 PKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ADN or .ADN2 or .ADN3 or :3ADN;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:96 or .A:109 or .A:111 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: LY333531 | Ligand Info | |||||
| Structure Description | Structure of human PDK1 kinase domain in complex with LY333531 | PDB:1UU3 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [2] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLFV 243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR283 AGNEYLIFQK 293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY333 GPLKAHPFFE 343 SVTWENLHQQ353 TPPKLTA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LY4 or .LY42 or .LY43 or :3LY4;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU88
3.283
GLY89
3.609
GLU90
4.023
GLY91
3.872
VAL96
4.115
ALA109
3.370
LYS111
3.563
GLU130
3.556
VAL143
3.449
LEU159
3.584
SER160
2.843
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| Ligand Name: UCN-01 | Ligand Info | |||||
| Structure Description | Structure of human PDK1 kinase domain in complex with UCN-01 | PDB:1OKZ | ||||
| Method | X-ray diffraction | Resolution | 2.51 Å | Mutation | No | [3] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLNF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .UCN or .UCN2 or .UCN3 or :3UCN;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:220 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU88
3.175
GLY89
3.178
GLU90
4.070
GLY91
4.801
VAL96
3.662
ALA109
3.280
LYS111
3.649
GLU130
4.675
VAL143
3.668
LEU159
3.808
SER160
2.925
TYR161
3.367
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| Ligand Name: O-Phosphoethanolamine | Ligand Info | |||||
| Structure Description | Crystal Structure of the Phosphoinositide-dependent Kinase-1 (PDK-1)Catalytic Domain bound to a dibenzonaphthyridine inhibitor | PDB:2R7B | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [4] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLFVGT 245 AQYVSPELLT255 EKSACKSSDL265 WALGCIIYQL275 VAGLPPFRAG285 NEYLIFQKII 295 KLEYDFPEKF305 FPKARDLVEK315 LLVLDATKRL325 GCEEMEGYGP335 LKAHPFFESV 345 TWENLHQQTP355 PKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PSE or .PSE2 or .PSE3 or :3PSE;style chemicals stick;color identity;select .A:126 or .A:129 or .A:204 or .A:228 or .A:242 or .A:243 or .A:253 or .A:257; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: DTD | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the PIF-Pocket | PDB:5LVO | ||||
| Method | X-ray diffraction | Resolution | 1.09 Å | Mutation | Yes | [1] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSP 232 ESKQARANFV243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR 283 AGNEGLIFAK293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY 333 GPLKAHPFFE343 SVTWENLHQQ353 TPPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DTD or .DTD2 or .DTD3 or :3DTD;style chemicals stick;color identity;select .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:249 or .A:253 or .A:254 or .A:287 or .A:291; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-serine-O-phosphate | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the PIF-Pocket | PDB:5LVO | ||||
| Method | X-ray diffraction | Resolution | 1.09 Å | Mutation | Yes | [1] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSP 232 ESKQARANFV243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR 283 AGNEGLIFAK293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY 333 GPLKAHPFFE343 SVTWENLHQQ353 TPPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SEP or .SEP2 or .SEP3 or :3SEP;style chemicals stick;color identity;select .A:126 or .A:129 or .A:204 or .A:227 or .A:228 or .A:239 or .A:240 or .A:242 or .A:243 or .A:253; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2,6-Dihydroanthra/1,9-Cd/Pyrazol-6-One | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Compound PS653 Bound to the ATP-Binding Site | PDB:5LVL | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [1] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFTFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLSPE 233 SKQARANFVG244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA 284 GNEGLIFAKI294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG 334 PLKAHPFFES344 VTWENLHQQT354 PPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .537 or .5372 or .5373 or :3537;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:165 or .A:166 or .A:169 or .A:212 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: S,S-(2-Hydroxyethyl)Thiocysteine | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket | PDB:4AW0 | ||||
| Method | X-ray diffraction | Resolution | 1.43 Å | Mutation | Yes | [5] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQARANFVGT245 AQYVSPELLT255 EKSAKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EGLIFAKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CME or .CME2 or .CME3 or :3CME;style chemicals stick;color identity;select .A:202 or .A:230 or .A:237 or .A:238 or .A:239 or .A:252 or .A:258 or .A:259 or .A:261 or .A:262 or .A:263 or .A:264 or .A:321 or .A:322; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Staurosporine | Ligand Info | |||||
| Structure Description | Structure of human PDK1 kinase domain in complex with staurosporine | PDB:1OKY | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
PQPRKKRPED
81 FKFGKILGEG91 SFSTVVLARE101 LATSREYAIK111 ILEKRHIIKE121 NKVPYVTRER 131 DVMSRLDHPF141 FVKLYFTFQD151 DEKLYFGLSY161 AKNGELLKYI171 RKIGSFDETC 181 TRFYTAEIVS191 ALEYLHGKGI201 IHRDLKPENI211 LLNEDMHIQI221 TDFGTAKVLS 231 PANFVGTAQY248 VSPELLTEKS258 ACKSSDLWAL268 GCIIYQLVAG278 LPPFRAGNEY 288 LIFQKIIKLE298 YDFPEKFFPK308 ARDLVEKLLV318 LDATKRLGCE328 EMEGYGPLKA 338 HPFFESVTWE348 NLHQQTPPKL358 TA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .STU or .STU2 or .STU3 or :3STU;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:93 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU88
3.370
GLY89
3.205
GLU90
4.005
PHE93
4.594
VAL96
3.622
ALA109
3.426
LYS111
3.397
GLU130
4.228
VAL143
4.196
LEU159
3.857
SER160
3.057
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| Ligand Name: Bisindolylmaleimide-I | Ligand Info | |||||
| Structure Description | Structure of human PDK1 kinase domain in complex with BIM-1 | PDB:1UU8 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [2] |
| PDB Sequence |
PQPRKKRPED
81 FKFGKILGEG91 SFSTVVLARE101 LATSREYAIK111 ILEKRHIIKE121 NKVPYVTRER 131 DVMSRLDHPF141 FVKLYFTFQD151 DEKLYFGLSY161 AKNGELLKYI171 RKIGSFDETC 181 TRFYTAEIVS191 ALEYLHGKGI201 IHRDLKPENI211 LLNEDMHIQI221 TDFGTAKVLS 231 NFVGTAQYVS250 PELLTEKSAC260 KSSDLWALGC270 IIYQLVAGLP280 PFRAGNEYLI 290 FQKIIKLEYD300 FPEKFFPKAR310 DLVEKLLVLD320 ATKRLGCEEM330 EGYGPLKAHP 340 FFESVTWENL350 HQQTPPKL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BI1 or .BI12 or .BI13 or :3BI1;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Inositol 1,3,4,5-Tetrakisphosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol (1,3,4,5)-tetrakisphosphate | PDB:1W1D | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [6] |
| PDB Sequence |
PLGSNIEQYI
416 HDLDSNSFEL426 DLQFSEDEKR436 LLLEKQAGGN446 PWHQFVENNL456 ILKMGPVDKR 466 KGLFARRRQL476 LLTEGPHLYY486 VDPVNKVLKG496 EIPWSQELRP506 EAKNFKTFFV 516 HTPNRTYYLM526 DPSGNAHKWC536 RKIQEVWRQR546 YQSH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4IP or .4IP2 or .4IP3 or :34IP;style chemicals stick;color identity;select .A:465 or .A:467 or .A:472 or .A:474 or .A:486 or .A:495 or .A:521 or .A:523; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(1h-Indol-3-Yl)-4-{1-[2-(1-Methylpyrrolidin-2-Yl)ethyl]-1h-Indol-3-Yl}-1h-Pyrrole-2,5-Dione | Ligand Info | |||||
| Structure Description | PDK1 mutant bound to allosteric disulfide fragment activator 2A2 | PDB:3ORZ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [7] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFCFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLSFV 243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR283 AGNEYLIFQK 293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY333 GPLKAHPFFE 343 SVTWENLHQQ353 TPPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BI4 or .BI42 or .BI43 or :3BI4;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:96 or .A:109 or .A:111 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU88
3.065
GLY89
3.549
GLU90
3.826
GLY91
3.495
SER94
4.648
VAL96
3.936
ALA109
3.332
LYS111
3.647
GLU130
3.995
MET134
4.752
VAL143
3.641
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-[4-(3-Chlorophenyl)piperazin-1-Yl]-4-Oxobutane-1-Thiol | Ligand Info | |||||
| Structure Description | PDK1 mutant bound to allosteric disulfide fragment activator 2A2 | PDB:3ORZ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [7] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFCFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLSFV 243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR283 AGNEYLIFQK 293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY333 GPLKAHPFFE 343 SVTWENLHQQ353 TPPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2A2 or .2A22 or .2A23 or :32A2;style chemicals stick;color identity;select .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[4-(Naphthalen-1-Ylmethyl)piperazin-1-Yl]-4-Oxobutane-1-Thiol | Ligand Info | |||||
| Structure Description | PDK1 mutant bound to allosteric disulfide fragment activator JS30 | PDB:3OTU | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [7] |
| PDB Sequence |
KRPEDFKFGK
86 ILGESFSTVV97 LARELATSRE107 YAIKILEKRH117 IIKENKVPYV127 TRERDVMSRL 137 DHPFFVKLYF147 CFQDDEKLYF157 GLSYAKNGEL167 LKYIRKIGSF177 DETCTRFYTA 187 EIVSALEYLH197 GKGIIHRDLK207 PENILLNEDM217 HIQITDFGTA227 KVLSARANFV 243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR283 AGNEYLIFQK 293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY333 GPLKAHPFFE 343 SVTWENLHQQ353 TPPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .J30 or .J302 or .J303 or :3J30;style chemicals stick;color identity;select .A:115 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-Methyl-N-(2-Sulfanylethyl)-1-Benzofuran-3-Carboxamide | Ligand Info | |||||
| Structure Description | PDK1 mutant bound to allosteric disulfide fragment inhibitor 1F8 | PDB:3ORX | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [7] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFCFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQRANFVGTA246 QYVSPELLTE256 KSACKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EYLIFQKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1F8 or .1F82 or .1F83 or :31F8;style chemicals stick;color identity;select .A:76 or .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (3s,6r)-1-[2-Amino-6-(3-Amino-2h-Indazol-6-Yl)pyrimidin-4-Yl]-6-Methyl-N-Phenylpiperidine-3-Carboxamide | Ligand Info | |||||
| Structure Description | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with (2R,5S)-1-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-N-phenyl-3-piperidinecarboxamide | PDB:3QD0 | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [8] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q4 or .3Q42 or .3Q43 or :33Q4;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:93 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:126 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:212 or .A:222 or .A:223 or .A:224 or .A:225 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.954
GLY89
4.015
GLU90
3.857
GLY91
3.858
PHE93
4.192
SER94
3.956
THR95
4.922
VAL96
3.734
ALA109
3.339
LYS111
2.959
TYR126
3.706
GLU130
2.875
MET134
3.769
|
|||||
| Ligand Name: Tert-Butyl {(3r,6s)-1-[2-Amino-6-(3-Amino-2h-Indazol-6-Yl)pyrimidin-4-Yl]-6-Methylpiperidin-3-Yl}carbamate | Ligand Info | |||||
| Structure Description | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl {(3R,6S)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-3-piperidinyl}carbamate | PDB:3QD3 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [8] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SFVGTAQYVS250 PELLTEKSAC260 KSSDLWALGC270 IIYQLVAGLP280 PFRAGNEYLI 290 FQKIIKLEYD300 FPEKFFPKAR310 DLVEKLLVLD320 ATKRLGCEEM330 EGYGPLKAHP 340 FFESVTWENL350 HQQTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q5 or .3Q52 or .3Q53 or :33Q5;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:93 or .A:94 or .A:96 or .A:109 or .A:111 or .A:113 or .A:123 or .A:126 or .A:127 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:212 or .A:222 or .A:223 or .A:224 or .A:225; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.942
GLY89
4.520
GLU90
3.666
GLY91
3.716
PHE93
3.743
SER94
2.880
VAL96
3.554
ALA109
3.311
LYS111
2.874
LEU113
3.781
LYS123
4.463
TYR126
3.750
VAL127
4.126
|
|||||
| Ligand Name: (2s)-4-[2-Amino-6-(3-Amino-2h-Indazol-6-Yl)pyrimidin-4-Yl]-N-Phenylmorpholine-2-Carboxamide | Ligand Info | |||||
| Structure Description | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 4-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-N-phenyl-2-morpholinecarboxamide | PDB:3QCY | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [8] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSV 243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR283 AGNEYLIFQK 293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY333 GPLKAHPFFE 343 SVTWENLHQQ353 TPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q3 or .3Q32 or .3Q33 or :33Q3;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:92 or .A:93 or .A:94 or .A:96 or .A:109 or .A:111 or .A:126 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:212 or .A:222 or .A:223 or .A:224 or .A:225 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.948
GLY89
4.858
GLU90
3.480
GLY91
3.155
SER92
3.119
PHE93
3.522
SER94
4.256
VAL96
3.717
ALA109
3.362
LYS111
3.001
TYR126
3.916
GLU130
2.860
MET134
3.989
|
|||||
| Ligand Name: 2-(5-{[(2R)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine | Ligand Info | |||||
| Structure Description | PDK-1 in complex with the inhibitor Compound-8i | PDB:3IOP | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [9] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8I1 or .8I12 or .8I13 or :38I1;style chemicals stick;color identity;select .A:86 or .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:207 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS86
4.497
LEU88
3.358
GLY89
3.299
GLU90
3.664
GLY91
3.340
SER94
3.031
THR95
4.326
VAL96
3.666
ALA109
3.540
LYS111
2.902
GLU130
4.739
VAL143
3.410
LEU159
3.382
|
|||||
| Ligand Name: 6-{2-Amino-6-[(3r)-3-Methylmorpholin-4-Yl]pyrimidin-4-Yl}-2h-Indazol-3-Amine | Ligand Info | |||||
| Structure Description | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-{2-Amino-6-[(3R)-3-methyl-4-morpholinyl]-4-pyrimidinyl}-1H-indazol-3-amine | PDB:3QCX | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [8] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q2 or .3Q22 or .3Q23 or :33Q2;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:92 or .A:94 or .A:96 or .A:109 or .A:111 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:209 or .A:212 or .A:222 or .A:223 or .A:224; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.871
GLY89
4.203
GLU90
3.645
GLY91
3.464
SER92
4.844
SER94
3.758
VAL96
3.765
ALA109
3.312
LYS111
2.968
GLU130
2.816
MET134
3.834
|
|||||
| Ligand Name: Tert-Butyl {(3r,5r)-1-[2-Amino-6-(3-Amino-2h-Indazol-6-Yl)pyrimidin-4-Yl]-5-Methylpiperidin-3-Yl}carbamate | Ligand Info | |||||
| Structure Description | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl{(3R,5R)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-5-methyl-3-piperidinyl}carbamate | PDB:3QD4 | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [8] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q6 or .3Q62 or .3Q63 or :33Q6;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:93 or .A:94 or .A:96 or .A:109 or .A:111 or .A:113 or .A:123 or .A:126 or .A:127 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:212 or .A:222 or .A:223 or .A:224 or .A:225; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
4.090
GLY89
3.811
GLU90
3.672
GLY91
3.807
PHE93
3.803
SER94
2.724
VAL96
3.812
ALA109
3.356
LYS111
2.834
LEU113
4.055
LYS123
4.711
TYR126
3.661
VAL127
4.203
|
|||||
| Ligand Name: 2-(5-{[(2S)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine | Ligand Info | |||||
| Structure Description | PDK1 in complex with Compound 8h | PDB:3ION | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [9] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSVGT 245 AQYVSPELLT255 EKSACKSSDL265 WALGCIIYQL275 VAGLPPFRAG285 NEYLIFQKII 295 KLEYDFPEKF305 FPKARDLVEK315 LLVLDATKRL325 GCEEMEGYGP335 LKAHPFFESV 345 TWENLHQQTP355 PKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8H1 or .8H12 or .8H13 or :38H1;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:207 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.345
GLY89
3.601
GLU90
3.570
GLY91
3.577
SER94
3.179
THR95
4.866
VAL96
3.841
ALA109
3.465
LYS111
2.779
GLU130
4.744
VAL143
3.495
LEU159
3.382
SER160
2.902
|
|||||
| Ligand Name: 6-[2-Amino-6-(Morpholin-4-Yl)pyrimidin-4-Yl]-2h-Indazol-3-Amine | Ligand Info | |||||
| Structure Description | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-[2-Amino-6-(4-morpholinyl)-4-pyrimidinyl]-1H-indazol-3-amine | PDB:3QCS | ||||
| Method | X-ray diffraction | Resolution | 2.49 Å | Mutation | No | [8] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q1 or .3Q12 or .3Q13 or :33Q1;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:92 or .A:94 or .A:96 or .A:109 or .A:111 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:212 or .A:222 or .A:223 or .A:224; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.935
GLY89
4.752
GLU90
3.582
GLY91
3.352
SER92
4.967
SER94
3.924
VAL96
3.403
ALA109
3.360
LYS111
2.698
GLU130
2.948
MET134
4.070
|
|||||
| Ligand Name: 6-(3-Amino-2h-Indazol-6-Yl)-N~4~-Ethylpyrimidine-2,4-Diamine | Ligand Info | |||||
| Structure Description | Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-(3-Amino-1H-indazol-6-yl)-N4-ethyl-2,4-pyrimidinediamine | PDB:3QCQ | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [8] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q0 or .3Q02 or .3Q03 or :33Q0;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:96 or .A:109 or .A:111 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:212 or .A:222 or .A:223 or .A:224; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 10,11-Dimethoxy-4-methyldibenzo[c,f]-2,7-naphthyridine-3,6-diamine | Ligand Info | |||||
| Structure Description | Crystal Structure of the Phosphoinositide-dependent Kinase-1 (PDK-1)Catalytic Domain bound to a dibenzonaphthyridine inhibitor | PDB:2R7B | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [4] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLFVGT 245 AQYVSPELLT255 EKSACKSSDL265 WALGCIIYQL275 VAGLPPFRAG285 NEYLIFQKII 295 KLEYDFPEKF305 FPKARDLVEK315 LLVLDATKRL325 GCEEMEGYGP335 LKAHPFFESV 345 TWENLHQQTP355 PKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .253 or .2532 or .2533 or :3253;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 1-(4-Chlorophenethyl)-2-(2-Chlorophenyl)-6-Oxopiperidine-3-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the PIF-Pocket | PDB:5ACK | ||||
| Method | X-ray diffraction | Resolution | 1.24 Å | Mutation | Yes | [10] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSP 232 ESKQARANFV243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR 283 AGNEGLIFAK293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY 333 GPLKAHPFFE343 SVTWENLHQQ353 TPPKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SVQ or .SVQ2 or .SVQ3 or :3SVQ;style chemicals stick;color identity;select .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: [(1r)-3-(4-Chlorophenyl)-3-Oxo-1-Phenylpropyl]propanedioic Acid | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket | PDB:4AW0 | ||||
| Method | X-ray diffraction | Resolution | 1.43 Å | Mutation | Yes | [5] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQARANFVGT245 AQYVSPELLT255 EKSAKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EGLIFAKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MJF or .MJF2 or .MJF3 or :3MJF;style chemicals stick;color identity;select .A:76 or .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: N-(6-Chloro-1,3-Benzothiazol-2-Yl)-1-Benzothiophene-2-Sulfonamide | Ligand Info | |||||
| Structure Description | Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RS2 | PDB:4RQV | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | Yes | [11] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SPESKQARAN240 FVGTAQYVSP251 ELLTEKSACK261 SSDLWALGCI271 IYQLVAGLPP 281 FRAGNEGLIF291 AKIIKLEYDF301 PEKFFPKARD311 LVEKLLVLDA321 TKRLGCEEME 331 GYGPLKAHPF341 FESVTWENLH351 QQTPPKLT
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .R2S or .R2S2 or .R2S3 or :3R2S;style chemicals stick;color identity;select .A:113 or .A:114 or .A:115 or .A:116 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: N-(6-Chloro-1,3-Benzothiazol-2-Yl)-1-Benzothiophene-3-Sulfonamide | Ligand Info | |||||
| Structure Description | Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RS1 | PDB:4RQK | ||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | Yes | [11] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFTFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLSPE 233 SKQARANFVG244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA 284 GNEGLIFAKI294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG 334 PLKAHPFFES344 VTWENLHQQT354 PPKLT
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .R1S or .R1S2 or .R1S3 or :3R1S;style chemicals stick;color identity;select .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: {(1r)-3-Oxo-1-Phenyl-3-[4-(Trifluoromethyl)phenyl]propyl}propanedioic Acid | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the PIF-Pocket | PDB:4AW1 | ||||
| Method | X-ray diffraction | Resolution | 1.68 Å | Mutation | Yes | [5] |
| PDB Sequence |
QHAQPPPRKK
77 RPEDFKFGKI87 LGEGSFSTVV97 LARELATSRE107 YAIKILEKRH117 IIKENKVPYV 127 TRERDVMSRL137 DHPFFVKLYF147 TFQDDEKLYF157 GLSYAKNGEL167 LKYIRKIGSF 177 DETCTRFYTA187 EIVSALEYLH197 GKGIIHRDLK207 PENILLNEDM217 HIQITDFGTA 227 KVLSARANFV243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR 283 AGNEGLIFAK293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY 333 GPLKAHPFFE343 SVTWENLHQQ353 TPPKLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .21O or .21O2 or .21O3 or :321O;style chemicals stick;color identity;select .A:76 or .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 3-(1-Benzyl-1h-1,2,3-Triazol-4-Yl)-1h-Pyrrolo[2,3-B]pyridine | Ligand Info | |||||
| Structure Description | Rapid preparation of triazolyl substituted NH-heterocyclic kinase inhibitors via one-pot Sonogashira coupling TMS-deprotection CuAAC sequence | PDB:3RCJ | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [12] |
| PDB Sequence |
KRPEDFKFGK
86 ILGEGSFSTV96 VLARELATSR106 EYAIKILEKR116 HIIKENKVPY126 VTRERDVMSR 136 LDHPFFVKLY146 FTFQDDEKLY156 FGLSYAKNGE166 LLKYIRKIGS176 FDETCTRFYT 186 AEIVSALEYL196 HGKGIIHRDL206 KPENILLNED216 MHIQITDFGT226 AKVLSPESKQ 236 ARANFVGTAQ247 YVSPELLTEK257 SACKSSDLWA267 LGCIIYQLVA277 GLPPFRAGNE 287 GLIFAKIIKL297 EYDFPEKFFP307 KARDLVEKLL317 VLDATKRLGC327 EEMEGYGPLK 337 AHPFFESVTW347 ENLHQQTPPK357 L
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3RC or .3RC2 or .3RC3 or :33RC;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: PDK1 inhibitor | Ligand Info | |||||
| Structure Description | PDK1 in complex with inhibitor MP7 | PDB:3NAX | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [13] |
| PDB Sequence |
KKRPEDFKFG
85 KILGEGSFST95 VVLARELATS105 REYAIKILEK115 RHIIKENKVP125 YVTRERDVMS 135 RLDHPFFVKL145 YFTFQDDEKL155 YFGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLSPESK 235 QARAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKLTA
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MP7 or .MP72 or .MP73 or :3MP7;style chemicals stick;color identity;select .A:88 or .A:91 or .A:92 or .A:94 or .A:96 or .A:109 or .A:111 or .A:125 or .A:126 or .A:134 or .A:135 or .A:137 or .A:142 or .A:143 or .A:145 or .A:159 or .A:160 or .A:161 or .A:162 or .A:196 or .A:201 or .A:202 or .A:203 or .A:212 or .A:221 or .A:222 or .A:223 or .A:224 or .A:225 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.952
GLY91
3.412
SER92
4.436
SER94
3.661
VAL96
4.022
ALA109
3.255
LYS111
2.679
PRO125
3.703
TYR126
3.403
MET134
3.545
SER135
4.295
LEU137
4.195
PHE142
3.360
VAL143
3.269
LEU145
4.654
|
|||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2z)-3-(Biphenyl-4-Yl)-5-(4-Chlorophenyl)pent-2-Enoic Acid | Ligand Info | |||||
| Structure Description | Human PDK1-PKCzeta Kinase Chimera in Complex with Allosteric Compound PS315 Bound to the PIF-Pocket | PDB:4CT1 | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [14] |
| PDB Sequence |
KKRPEDFKFG
85 KILGEGSFST95 VVLARELATS105 REYAIKIVEK115 RHVHKENKIP125 YVQREKDVMS 135 RLDHPFFVKL145 YFCFQDDEKL155 YLGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLSPESK 235 QARANFVGTA246 QYVSPELLTE256 KSACKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EGLIFAKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .31S or .31S2 or .31S3 or :331S;style chemicals stick;color identity;select .A:76 or .A:94 or .A:111 or .A:112 or .A:113 or .A:115 or .A:118 or .A:124 or .A:126 or .A:127 or .A:128 or .A:130 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (3s)-3-(4-Chlorophenyl)-4-(5,7-Dichloro-1h-Benzimidazol-2-Yl)butanoic Acid | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Activator PS171 Bound to the PIF-Pocket | PDB:4A07 | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [15] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQARANFVGT245 AQYVSPELLT255 EKSAKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EGLIFAKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AZ7 or .AZ72 or .AZ73 or :3AZ7;style chemicals stick;color identity;select .A:76 or .A:113 or .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157 or .A:168 or .A:171 or .A:172 or .A:175 or .A:209 or .A:247 or .A:248 or .A:274 or .A:278 or .A:279 or .A:280 or .A:282 or .A:283 or .A:284 or .A:290; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS76
2.447
LEU113
3.926
LYS115
2.763
ILE118
3.821
ILE119
2.628
VAL124
2.748
VAL127
2.923
THR128
3.410
ARG131
2.992
THR148
2.683
PHE149
3.432
GLN150
3.109
LEU155
2.569
TYR156
3.648
PHE157
2.981
|
|||||
| Ligand Name: Thiocysteine | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Activator PS171 Bound to the PIF-Pocket | PDB:4A07 | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [15] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQARANFVGT245 AQYVSPELLT255 EKSAKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EGLIFAKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSS or .CSS2 or .CSS3 or :3CSS;style chemicals stick;color identity;select .A:202 or .A:204 or .A:230 or .A:237 or .A:238 or .A:239 or .A:252 or .A:258 or .A:259 or .A:261 or .A:262 or .A:263 or .A:264 or .A:321 or .A:322 or .A:324; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (2z)-5-(4-Chlorophenyl)-3-Phenylpent-2-Enoic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of Human PDK1 kinase domain in complex with an allosteric activator bound to the PIF-pocket | PDB:3HRF | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [16] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQARANFVGT245 AQYVSPELLT255 EKSACKSSDL265 WALGCIIYQL275 VAGLPPFRAG 285 NEGLIFAKII295 KLEYDFPEKF305 FPKARDLVEK315 LLVLDATKRL325 GCEEMEGYGP 335 LKAHPFFESV345 TWENLHQQTP355 PKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P47 or .P472 or .P473 or :3P47;style chemicals stick;color identity;select .A:76 or .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: [4-Amino-7-(Propan-2-Yl)-7h-Pyrrolo[2,3-D]pyrimidin-5-Yl](6-{[(3s,4r)-4-(4-Fluorophenyl)tetrahydrofuran-3-Yl]amino}pyrazin-2-Yl)methanone | Ligand Info | |||||
| Structure Description | Discovery of a Novel, Potent and Selective Inhibitor of 3-Phosphoinositide Dependent Kinase (PDK1) | PDB:3RWP | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [17] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ABQ or .ABQ2 or .ABQ3 or :3ABQ;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:207 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.360
GLY89
3.021
GLU90
3.540
GLY91
3.343
SER94
3.287
THR95
3.503
VAL96
3.140
ALA109
3.571
LYS111
2.693
GLU130
4.366
VAL143
3.921
LEU159
3.479
|
|||||
| Ligand Name: (3R)-4-(6-chloro-1H-benzimidazol-2-yl)-3-(4-chlorophenyl)butanoic acid | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Activator PS114 Bound to the PIF-Pocket | PDB:4A06 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [15] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSPES 234 KQARANFVGT245 AQYVSPELLT255 EKSACKSSDL265 WALGCIIYQL275 VAGLPPFRAG 285 NEGLIFAKII295 KLEYDFPEKF305 FPKARDLVEK315 LLVLDATKRL325 GCEEMEGYGP 335 LKAHPFFESV345 TWENLHQQTP355 PKLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .A06 or .A062 or .A063 or :3A06;style chemicals stick;color identity;select .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-(1H-imidazol-1-yl)-9-methoxy-8-(2-methoxyethoxy)benzo[c][2,7]naphthyridin-4-amine | Ligand Info | |||||
| Structure Description | Phosphoinositide-dependent protein kinase 1 (PDK-1) in complex with compound 9 | PDB:3H9O | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [18] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLSFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9BD or .9BD2 or .9BD3 or :39BD;style chemicals stick;color identity;select .A:88 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:169 or .A:212 or .A:220 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: [4-Amino-7-(Propan-2-Yl)-7h-Pyrrolo[2,3-D]pyrimidin-5-Yl](6-{[2-(Pyridin-3-Yl)ethyl]amino}pyrazin-2-Yl)methanone | Ligand Info | |||||
| Structure Description | Discovery of a Novel, Potent and Selective Inhibitor of 3-Phosphoinositide Dependent Kinase (PDK1) | PDB:3RWQ | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [17] |
| PDB Sequence |
PQPRKKRPED
81 FKFGKILGEG91 SFSTVVLARE101 LATSREYAIK111 ILEKRHIIKE121 NKVPYVTRER 131 DVMSRLDHPF141 FVKLYFTFQD151 DEKLYFGLSY161 AKNGELLKYI171 RKIGSFDETC 181 TRFYTAEIVS191 ALEYLHGKGI201 IHRDLKPENI211 LLNEDMHIQI221 TDFGTAKVLS 231 PARANFVGTA246 QYVSPELLTE256 KSACKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EYLIFQKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3RW or .3RW2 or .3RW3 or :33RW;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.350
GLY89
3.415
GLU90
3.623
GLY91
3.583
SER94
3.253
THR95
4.503
VAL96
3.499
ALA109
3.616
LYS111
2.897
GLU130
4.381
VAL143
3.839
|
|||||
| Ligand Name: 6-[2-(Hydroxymethyl)phenyl]isoquinolin-1(2h)-One | Ligand Info | |||||
| Structure Description | Novel Isoquinolone PDK1 Inhibitors Discovered through Fragment-Based Lead Discovery | PDB:3SC1 | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [19] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSN 240 FVGTAQYVSP251 ELLTEKSACK261 SSDLWALGCI271 IYQLVAGLPP281 FRAGNEYLIF 291 QKIIKLEYDF301 PEKFFPKARD311 LVEKLLVLDA321 TKRLGCEEME331 GYGPLKAHPF 341 FESVTWENLH351 QQTPPKLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3S1 or .3S12 or .3S13 or :33S1;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:96 or .A:109 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:166 or .A:209 or .A:212 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: N-[2-({6-[(2-Sulfanylethyl)amino]pyrimidin-4-Yl}amino)ethyl]propanamide | Ligand Info | |||||
| Structure Description | Crystal structure of an extender (SPD28345)-modified human PDK1 complex 2 | PDB:3PWY | ||||
| Method | X-ray diffraction | Resolution | 3.50 Å | Mutation | Yes | [20] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGCLLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SPSFVGTAQY248 VSPELLTEKS258 ASKSSDLWAL268 GCIIYQLVAG278 LPPFRAGNEY 288 LIFQKIIKLE298 YDFPEKFFPK308 ARDLVEKLLV318 LDATKRLGCE328 EMEGYGPLKA 338 HPFFESVTWE348 NLHQQTPPKL358 T
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SYP or .SYP2 or .SYP3 or :3SYP;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:209 or .A:212 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid | Ligand Info | |||||
| Structure Description | Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RF4 | PDB:4XX9 | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [21] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SPESKQARAN240 FVGTAQYVSP251 ELLTEKSACK261 SSDLWALGCI271 IYQLVAGLPP 281 FRAGNEGLIF291 AKIIKLEYDF301 PEKFFPKARD311 LVEKLLVLDA321 TKRLGCEEME 331 GYGPLKAHPF341 FESVTWENLH351 QQTPPKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RF4 or .RF42 or .RF43 or :3RF4;style chemicals stick;color identity;select .A:76 or .A:113 or .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157 or .A:168 or .A:171 or .A:172 or .A:173 or .A:175 or .A:274 or .A:278 or .A:279 or .A:280; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS76
1.944
LEU113
4.831
LYS115
2.937
ILE118
2.801
ILE119
2.972
VAL124
3.157
VAL127
2.813
THR128
3.788
ARG131
2.153
THR148
2.244
PHE149
2.520
GLN150
3.158
|
|||||
| Ligand Name: (2~{S})-1-(6-chloranyl-1,3-benzothiazol-2-yl)-4-oxidanyl-5-oxidanylidene-2-thiophen-2-yl-2~{H}-pyrrole-3-carboxylate | Ligand Info | |||||
| Structure Description | Human PDK1-PKCiota Kinase Chimera in Complex with Allosteric Compound PS267 Bound to the PIF-Pocket | PDB:5MRD | ||||
| Method | X-ray diffraction | Resolution | 1.41 Å | Mutation | Yes | [22] |
| PDB Sequence |
SKRPEDFKFG
85 KILGEGSFST95 VVLARELATS105 REYAIKIVEK115 RHVNKENKIP125 YVQREKDVMS 135 RLDHPFFVKL145 YFCFQDDEKL155 YFGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLSPESK 235 QARANFVGTA246 QYVSPELLTE256 KSACKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN 286 EGLIFAKIIK296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL 336 KAHPFFESVT346 WENLHQQTPP356 KLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .S26 or .S262 or .S263 or :3S26;style chemicals stick;color identity;select .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-(1H-Indol-3-YL)-4-(1-{2-[(2S)-1-methylpyrrolidinyl]ethyl}-1H-indol-3-YL)-1H-pyrrole-2,5-dione | Ligand Info | |||||
| Structure Description | Structure of human PDK1 kinase domain in complex with BIM-2 | PDB:1UU7 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [2] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSP 232 RANFVGTAQY248 VSPELLTEKS258 ACKSSDLWAL268 GCIIYQLVAG278 LPPFRAGNEY 288 LIFQKIIKLE298 YDFPEKFFPK308 ARDLVEKLLV318 LDATKRLGCE328 EMEGYGPLKA 338 HPFFESVTWE348 NLHQQTPPKL358 T
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BI2 or .BI22 or .BI23 or :3BI2;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 8-(Cyclohexa-2,5-dien-1-ylideneamino)-1-(piperidin-4-ylmethyl)-4,5-dihydro-1H-pyrazolo[4,3-H]quinazoline-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor | PDB:2XCH | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [23] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSN 240 FVGTAQYVSP251 ELLTEKSACK261 SSDLWALGCI271 IYQLVAGLPP281 FRAGNEYLIF 291 QKIIKLEYDF301 PEKFFPKARD311 LVEKLLVLDA321 TKRLGCEEME331 GYGPLKAHPF 341 FESVTWENLH351 QQTPPKLT
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CKG or .CKG2 or .CKG3 or :3CKG;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:209 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4-Ethyl-6-[5-(1h-Pyrazol-4-Yl)-1h-Pyrrolo[2,3-B]pyridin-3-Yl]pyrimidin-2-Amine | Ligand Info | |||||
| Structure Description | DISCOVERY OF NOVEL 7-AZAINDOLES AS PDK1 INHIBITORS | PDB:5HKM | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [24] |
| PDB Sequence |
KKRPEDFKFG
85 KILGEGSFST95 VVLARELATS105 REYAIKILEK115 RHIIKENKVP125 YVTRERDVMS 135 RLDHPFFVKL145 YFTFQDDEKL155 YFGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLFVGTA 246 QYVSPELLTE256 KSACKSSDLW266 ALGCIIYQLV276 AGLPPFRAGN286 EYLIFQKIIK 296 LEYDFPEKFF306 PKARDLVEKL316 LVLDATKRLG326 CEEMEGYGPL336 KAHPFFESVT 346 WENLHQQTPP356 KL
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .61Y or .61Y2 or .61Y3 or :361Y;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223 or .A:224; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.327
GLY89
4.455
GLU90
4.533
VAL96
3.681
ALA109
3.360
LYS111
3.694
GLU130
4.254
VAL143
4.542
LEU159
3.949
SER160
2.695
TYR161
3.758
|
|||||
| Ligand Name: 1-Methyl-8-{[4-(4-methylpiperazin-1-YL)phenyl]amino}-N-[(2-methylpyridin-4-YL)methyl]-4,5-dihydro-1H-pyrazolo[4,3-H]quinazoline-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor | PDB:2XCK | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [23] |
| PDB Sequence |
KKRPEDFKFG
85 KILGEGSFST95 TVLARELATS105 REYAIKILEK115 RHIIKENKVP125 YVTRERDVMS 135 RLDHPFFVKL145 YFTFQDDEKL155 YFGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLSNFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MH4 or .MH42 or .MH43 or :3MH4;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:165 or .A:166 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU88
3.556
GLY89
3.881
GLU90
3.851
GLY91
3.457
SER94
2.945
THR95
3.977
THR96
3.702
ALA109
3.315
LYS111
2.663
GLU130
4.565
VAL143
4.312
|
|||||
| Ligand Name: 4-Butyl-6-(1h-Pyrrolo[2,3-B]pyridin-3-Yl)pyrimidin-2-Amine | Ligand Info | |||||
| Structure Description | DISCOVERY OF NOVEL 7-AZAINDOLES AS PDK1 INHIBITORS | PDB:5HO8 | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [24] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SFVGTAQYVS250 PELLTEKSAC260 KSSDLWALGC270 IIYQLVAGLP280 PFRAGNEYLI 290 FQKIIKLEYD300 FPEKFFPKAR310 DLVEKLLVLD320 ATKRLGCEEM330 EGYGPLKAHP 340 FFESVTWENL350 HQQTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .63E or .63E2 or .63E3 or :363E;style chemicals stick;color identity;select .A:88 or .A:89 or .A:90 or .A:91 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 5-Amino-3-(Methylsulfanyl)-1h-Pyrazole-1,4-Dicarboxamide | Ligand Info | |||||
| Structure Description | DISCOVERY OF NOVEL 7-AZAINDOLES AS PDK1 INHIBITORS | PDB:5HO7 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [24] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SPFVGTAQYV249 SPELLTEKSA259 CKSSDLWALG269 CIIYQLVAGL279 PPFRAGNEYL 289 IFQKIIKLEY299 DFPEKFFPKA309 RDLVEKLLVL319 DATKRLGCEE329 MEGYGPLKAH 339 PFFESVTWEN349 LHQQTPPKLT359
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .63L or .63L2 or .63L3 or :363L;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:166 or .A:209 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 6-Methoxy-2-(1h-Pyrazol-5-Yl)-1h-Benzimidazole | Ligand Info | |||||
| Structure Description | DISCOVERY OF NOVEL 7-AZAINDOLES AS PDK1 INHIBITORS | PDB:5HNG | ||||
| Method | X-ray diffraction | Resolution | 3.01 Å | Mutation | No | [24] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SPFVGTAQYV249 SPELLTEKSA259 CKSSDLWALG269 CIIYQLVAGL279 PPFRAGNEYL 289 IFQKIIKLEY299 DFPEKFFPKA309 RDLVEKLLVL319 DATKRLGCEE329 MEGYGPLKAH 339 PFFESVTWEN349 LHQQTPPKLT359
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .62O or .62O2 or .62O3 or :362O;style chemicals stick;color identity;select .A:86 or .A:88 or .A:96 or .A:109 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:169 or .A:212 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 6-(2-Aminopyrimidin-4-Yl)-1h-Indazol-3-Amine | Ligand Info | |||||
| Structure Description | phosphoinositide-dependent kinase-1 (PDK1) with lead compound | PDB:3NUN | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [25] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SFVGTAQYVS250 PELLTEKSAC260 KSSDLWALGC270 IIYQLVAGLP280 PFRAGNEYLI 290 FQKIIKLEYD300 FPEKFFPKAR310 DLVEKLLVLD320 ATKRLGCEEM330 EGYGPLKAHP 340 FFESVTWENL350 HQQTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JMZ or .JMZ2 or .JMZ3 or :3JMZ;style chemicals stick;color identity;select .A:88 or .A:96 or .A:109 or .A:111 or .A:130 or .A:134 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:212 or .A:222 or .A:223 or .A:224; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-[1-(3-Aminopropyl)-1H-indol-3-YL]-4-(1-methyl-1H-indol-3-YL)-1H-pyrrole-2,5-dione | Ligand Info | |||||
| Structure Description | Structure of human PDK1 kinase domain in complex with BIM-8 | PDB:1UVR | ||||
| Method | X-ray diffraction | Resolution | 2.81 Å | Mutation | No | [2] |
| PDB Sequence |
PPQPRKKRPE
80 DFKFGKILGE90 GSFSTVVLAR100 ELATSREYAI110 KILEKRHIIK120 ENKVPYVTRE 130 RDVMSRLDHP140 FFVKLYFTFQ150 DDEKLYFGLS160 YAKNGELLKY170 IRKIGSFDET 180 CTRFYTAEIV190 SALEYLHGKG200 IIHRDLKPEN210 ILLNEDMHIQ220 ITDFGTAKVL 230 SPARANFVGT245 AQYVSPELLT255 EKSACKSSDL265 WALGCIIYQL275 VAGLPPFRAG 285 NEYLIFQKII295 KLEYDFPEKF305 FPKARDLVEK315 LLVLDATKRL325 GCEEMEGYGP 335 LKAHPFFESV345 TWENLHQQTP355 PKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BI8 or .BI82 or .BI83 or :3BI8;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-[1-(3-Aminopropyl)-1H-indol-3-YL]-4-(1H-indol-3-YL)-1H-pyrrole-2,5-dione | Ligand Info | |||||
| Structure Description | Structure of human PDK1 kinase domain in complex with BIM-3 | PDB:1UU9 | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [2] |
| PDB Sequence |
PQPRKKRPED
81 FKFGKILGEG91 SFSTVVLARE101 LATSREYAIK111 ILEKRHIIKE121 NKVPYVTRER 131 DVMSRLDHPF141 FVKLYFTFQD151 DEKLYFGLSY161 AKNGELLKYI171 RKIGSFDETC 181 TRFYTAEIVS191 ALEYLHGKGI201 IHRDLKPENI211 LLNEDMHIQI221 TDFGTAKVLN 240 FVGTAQYVSP251 ELLTEKSACK261 SSDLWALGCI271 IYQLVAGLPP281 FRAGNEYLIF 291 QKIIKLEYDF301 PEKFFPKARD311 LVEKLLVLDA321 TKRLGCEEME331 GYGPLKAHPF 341 FESVTWENLH351 QQTPPK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BI3 or .BI32 or .BI33 or :3BI3;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:165 or .A:166 or .A:169 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3,4-dihydroisoquinolin-1(2H)-one | Ligand Info | |||||
| Structure Description | phosphoinositide-dependent kinase-1 (PDK1) with fragment11 | PDB:3NUU | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [26] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JOZ or .JOZ2 or .JOZ3 or :3JOZ;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:212 or .A:220 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4-Hydroxyquinazoline | Ligand Info | |||||
| Structure Description | phosphoinositide-dependent kinase-1 (PDK1) with fragment17 | PDB:3NUY | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [26] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JPZ or .JPZ2 or .JPZ3 or :3JPZ;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:212 or .A:220 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-[5-({5-[(Aminocarbonyl)amino]-2-Oxo-2h-Indol-3-Yl}methyl)-1h-Pyrrol-3-Yl]-N-(2-Piperidin-1-Ylethyl)benzamide | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 3-{5-[2-Oxo-5-ureido-1,2-dihydro-indol-(3Z)-ylidenemethyl]-1H-pyrrol-3-yl}-N-(2-piperidin-1-yl-ethyl)-benzamide COMPLEX | PDB:2PE2 | ||||
| Method | X-ray diffraction | Resolution | 2.13 Å | Mutation | Yes | [27] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFTFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLT
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .464 or .4642 or .4643 or :3464;style chemicals stick;color identity;select .A:88 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:169 or .A:170 or .A:173 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU88
3.844
VAL96
3.834
ALA109
3.245
LYS111
2.766
GLU130
4.537
VAL143
4.293
LEU159
3.892
SER160
2.787
TYR161
3.402
ALA162
2.769
LYS163
3.687
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| Ligand Name: 1-{2-Oxo-3-[(1r)-1-(1h-Pyrrol-2-Yl)ethyl]-2h-Indol-5-Yl}urea | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) {2-Oxo-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-2,3-dihydro-1H-indol-5-yl}-urea {BX-517} COMPLEX | PDB:2PE1 | ||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | Yes | [28] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFTFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLT
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .517 or .5172 or .5173 or :3517;style chemicals stick;color identity;select .A:88 or .A:89 or .A:94 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:210 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Propanediamide, N-(3-((5-bromo-2-((3-((1-pyrrolidinylcarbonyl)amino)phenyl)amino)-4-pyrimidinyl)amino)propyl)-2,2-dimethyl- | Ligand Info | |||||
| Structure Description | Crystal Structure Of N1-[3-[[5-bromo-2-[[3-[(1-pyrrolidinylcarbonyl)amino]phenyl]amino]-4-pyrimidinyl]amino]propyl]-2,2-dimethylpropanediamide Complexed with Human PDK1 | PDB:1Z5M | ||||
| Method | X-ray diffraction | Resolution | 2.17 Å | Mutation | Yes | [29] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFTFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LI8 or .LI82 or .LI83 or :3LI8;style chemicals stick;color identity;select .A:86 or .A:88 or .A:89 or .A:90 or .A:91 or .A:94 or .A:95 or .A:96 or .A:109 or .A:111 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:169 or .A:209 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS86
4.628
LEU88
2.854
GLY89
2.797
GLU90
3.045
GLY91
3.427
SER94
3.067
THR95
4.548
VAL96
3.307
ALA109
3.380
LYS111
3.615
VAL143
4.093
LEU159
3.248
|
|||||
| Ligand Name: 5-Hydroxy-3-[(1r)-1-(1h-Pyrrol-2-Yl)ethyl]-2h-Indol-2-One | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 5-Hydroxy-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-1,3-dihydro-indol-2-one COMPLEX | PDB:2PE0 | ||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | Yes | [28] |
| PDB Sequence |
PRKKRPEDFK
83 FGKILGEGSF93 STVVLARELA103 TSREYAIKIL113 EKRHIIKENK123 VPYVTRERDV 133 MSRLDHPFFV143 KLYFTFQDDE153 KLYFGLSYAK163 NGELLKYIRK173 IGSFDETCTR 183 FYTAEIVSAL193 EYLHGKGIIH203 RDLKPENILL213 NEDMHIQITD223 FGTAKVLFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLT
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .39Z or .39Z2 or .39Z3 or :339Z;style chemicals stick;color identity;select .A:88 or .A:89 or .A:96 or .A:109 or .A:111 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:212 or .A:222 or .A:223; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1H-Indazol-3-amine | Ligand Info | |||||
| Structure Description | phosphoinositide-dependent kinase-1 (PDK1) with fragment8 | PDB:3NUS | ||||
| Method | X-ray diffraction | Resolution | 2.75 Å | Mutation | No | [26] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSF 242 VGTAQYVSPE252 LLTEKSACKS262 SDLWALGCII272 YQLVAGLPPF282 RAGNEYLIFQ 292 KIIKLEYDFP302 EKFFPKARDL312 VEKLLVLDAT322 KRLGCEEMEG332 YGPLKAHPFF 342 ESVTWENLHQ352 QTPPKL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JNZ or .JNZ2 or .JNZ3 or :3JNZ;style chemicals stick;color identity;select .A:88 or .A:96 or .A:109 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:212 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Phosphatidylinositol 3,4,5-trsiphosphate | Ligand Info | |||||
| Structure Description | Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate | PDB:1W1G | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [6] |
| PDB Sequence |
PLGSNIEQYI
416 HDLDSNSFEL426 DLQFSEDEKR436 LLLEKQAGGN446 PWHQFVENNL456 ILKMGPVDKR 466 KGLFARRRQL476 LLTEGPHLYY486 VDPVNKVLKG496 EIPWSQELRP506 EAKNFKTFFV 516 HTPNRTYYLM526 DPSGNAHKWC536 RKIQEVWRQR546 YQSH
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4PT or .4PT2 or .4PT3 or :34PT;style chemicals stick;color identity;select .A:465 or .A:467 or .A:472 or .A:474 or .A:486 or .A:495 or .A:521 or .A:523; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-(2-cyclopropylethylidene)-9-(1H-pyrazol-4-yl)-6-{[(1R)-1,2,2-trimethylpropyl]amino}benzo[c][1,6]naphthyridin-1(4H)-one | Ligand Info | |||||
| Structure Description | PDK1 in complex with inhibitor MP6 | PDB:3NAY | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [30] |
| PDB Sequence |
KKRPEDFKFG
85 KILGEGSFST95 VVLARELATS105 REYAIKILEK115 RHIIKENKVP125 YVTRERDVMS 135 RLDHPFFVKL145 YFTFQDDEKL155 YFGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLSNFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEYLIFQKI 294 IKLEYDFPEK304 FFPKARDLVE314 KLLVLDATKR324 LGCEEMEGYG334 PLKAHPFFES 344 VTWENLHQQT354 PPKLTAYL
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MP6 or .MP62 or .MP63 or :3MP6;style chemicals stick;color identity;select .A:86 or .A:88 or .A:89 or .A:90 or .A:91 or .A:96 or .A:109 or .A:111 or .A:130 or .A:143 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:209 or .A:210 or .A:212 or .A:222 or .A:223; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS86
4.071
LEU88
3.384
GLY89
3.887
GLU90
3.282
GLY91
4.443
VAL96
3.483
ALA109
3.176
LYS111
3.445
GLU130
3.441
VAL143
3.893
LEU159
3.755
SER160
2.717
|
|||||
| Ligand Name: 2-oxidanylidenepropyl ~{N}-(2-chloranyl-6-fluoranyl-phenyl)carbonyl-~{N}'-(4-chlorophenyl)carbamimidothioate | Ligand Info | |||||
| Structure Description | Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the PIF-Pocket | PDB:5LVO | ||||
| Method | X-ray diffraction | Resolution | 1.09 Å | Mutation | Yes | [1] |
| PDB Sequence |
QPRKKRPEDF
82 KFGKILGEGS92 FSTVVLAREL102 ATSREYAIKI112 LEKRHIIKEN122 KVPYVTRERD 132 VMSRLDHPFF142 VKLYFTFQDD152 EKLYFGLSYA162 KNGELLKYIR172 KIGSFDETCT 182 RFYTAEIVSA192 LEYLHGKGII202 HRDLKPENIL212 LNEDMHIQIT222 DFGTAKVLSP 232 ESKQARANFV243 GTAQYVSPEL253 LTEKSACKSS263 DLWALGCIIY273 QLVAGLPPFR 283 AGNEGLIFAK293 IIKLEYDFPE303 KFFPKARDLV313 EKLLVLDATK323 RLGCEEMEGY 333 GPLKAHPFFE343 SVTWENLHQQ353 TPPKLT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .78W or .78W2 or .78W3 or :378W;style chemicals stick;color identity;select .A:113 or .A:115 or .A:118 or .A:119 or .A:124 or .A:127 or .A:128 or .A:131 or .A:148 or .A:149 or .A:150 or .A:155 or .A:156 or .A:157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol. 2016 Oct 20;23(10):1193-1205. | ||||
| REF 2 | Interactions of LY333531 and other bisindolyl maleimide inhibitors with PDK1. Structure. 2004 Feb;12(2):215-26. | ||||
| REF 3 | Structural basis for UCN-01 (7-hydroxystaurosporine) specificity and PDK1 (3-phosphoinositide-dependent protein kinase-1) inhibition. Biochem J. 2003 Oct 15;375(Pt 2):255-62. | ||||
| REF 4 | Discovery of dibenzo[c,f][2,7]naphthyridines as potent and selective 3-phosphoinositide-dependent kinase-1 inhibitors. J Med Chem. 2007 Nov 15;50(23):5547-9. | ||||
| REF 5 | Substrate-selective inhibition of protein kinase PDK1 by small compounds that bind to the PIF-pocket allosteric docking site. Chem Biol. 2012 Sep 21;19(9):1152-63. | ||||
| REF 6 | Structural insights into the regulation of PDK1 by phosphoinositides and inositol phosphates. EMBO J. 2004 Oct 13;23(20):3918-28. | ||||
| REF 7 | Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6056-61. | ||||
| REF 8 | Structure-based design of potent and selective 3-phosphoinositide-dependent kinase-1 (PDK1) inhibitors. J Med Chem. 2011 Mar 24;54(6):1871-95. | ||||
| REF 9 | The identification of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7]naphthyridin-4-ylamines as potent inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1). Eur J Med Chem. 2010 Apr;45(4):1379-86. | ||||
| REF 10 | Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angew Chem Int Ed Engl. 2015 Nov 16;54(47):13933-6. | ||||
| REF 11 | A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18590-5. | ||||
| REF 12 | Rapid preparation of triazolyl substituted NH-heterocyclic kinase inhibitors via one-pot Sonogashira coupling-TMS-deprotection-CuAAC sequence. Org Biomol Chem. 2011 Jul 21;9(14):5129-36. | ||||
| REF 13 | Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor. J Biol Chem. 2011 Feb 25;286(8):6433-48. | ||||
| REF 14 | Molecular mechanism of regulation of the atypical protein kinase C by N-terminal domains and an allosteric small compound. Chem Biol. 2014 Jun 19;21(6):754-65. | ||||
| REF 15 | Allosteric regulation of protein kinase PKCZeta by the N-terminal C1 domain and small compounds to the PIF-pocket. Chem Biol. 2011 Nov 23;18(11):1463-73. | ||||
| REF 16 | Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1. Nat Chem Biol. 2009 Oct;5(10):758-64. | ||||
| REF 17 | Discovery of novel, potent, and selective inhibitors of 3-phosphoinositide-dependent kinase (PDK1). J Med Chem. 2011 Dec 22;54(24):8490-500. | ||||
| REF 18 | Benzo[c][2,7]naphthyridines as inhibitors of PDK-1. Bioorg Med Chem Lett. 2009 Sep 1;19(17):5225-8. | ||||
| REF 19 | Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery. J Comput Aided Mol Des. 2011 Jul;25(7):689-98. | ||||
| REF 20 | Discovery of a potent and highly selective PDK1 inhibitor via fragment-based drug discovery. Bioorg Med Chem Lett. 2011 May 15;21(10):3078-83. | ||||
| REF 21 | Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem. 2015 Oct 22;58(20):8285-8291. | ||||
| REF 22 | An Allosteric Inhibitor Scaffold Targeting the PIF-Pocket of Atypical Protein Kinase C Isoforms. ACS Chem Biol. 2017 Feb 17;12(2):564-573. | ||||
| REF 23 | Structure-based optimization of potent PDK1 inhibitors. Bioorg Med Chem Lett. 2010 Jul 15;20(14):4095-9. | ||||
| REF 24 | Discovery of novel 7-azaindoles as PDK1 inhibitors. Bioorg Med Chem Lett. 2016 Jul 1;26(13):3073-3080. | ||||
| REF 25 | Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery | ||||
| REF 26 | Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery. ACS Med Chem Lett. 2010 Jul 22;1(8):439-42. | ||||
| REF 27 | Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 2: optimization of BX-517. Bioorg Med Chem Lett. 2007 Jul 15;17(14):3819-25. | ||||
| REF 28 | Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: design, synthesis and biological activity. Bioorg Med Chem Lett. 2007 Jul 15;17(14):3814-8. | ||||
| REF 29 | Novel small molecule inhibitors of 3-phosphoinositide-dependent kinase-1. J Biol Chem. 2005 May 20;280(20):19867-74. | ||||
| REF 30 | Selective inhibition of PDK1 using an allosteric kinase inhibitor and RNAi impairs cancer cell migration and anchorage-independent growth of primary tumor lines | ||||
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