Target Binding Site Detail
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Adenosine triphosphate | Ligand Info | |||
| Canonical SMILES | C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N | ||||
| InChI | 1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 | ||||
| InChIKey | ZKHQWZAMYRWXGA-KQYNXXCUSA-N | ||||
| PubChem Compound ID | 5957 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5LVO Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the PIF-Pocket | ||||||
| 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
|
|||||
|
|
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
|
|||||
| PDB ID: 5ACK Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the PIF-Pocket | ||||||
| Method | X-ray diffraction | Resolution | 1.24 Å | Mutation | Yes | [2] |
| 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
|
|||||
|
|
LEU88
3.080
GLY89
2.429
GLU90
3.648
GLY91
2.767
SER92
2.191
PHE93
4.471
SER94
1.912
THR95
4.194
VAL96
2.750
ALA109
3.038
LYS111
2.680
TYR126
4.170
VAL143
2.790
|
|||||
| PDB ID: 4CT2 Human PDK1-PKCzeta Kinase Chimera | ||||||
| Method | X-ray diffraction | Resolution | 1.25 Å | Mutation | Yes | [3] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKIVE114 KRHVIPYVQR129 EKDVMSRLDH 139 PFFVKLYFCF149 QDDEKLYLGL159 SYAKNGELLK169 YIRKIGSFDE179 TCTRFYTAEI 189 VSALEYLHGK199 GIIHRDLKPE209 NILLNEDMHI219 QITDFGTAKV229 LSPESKQARA 239 NFVGTAQYVS250 PELLTEKSAC260 KSSDLWALGC270 IIYQLVAGLP280 PFRAGNEGLI 290 FAKIIKLEYD300 FPEKFFPKAR310 DLVEKLLVLD320 ATKRLGCEEM330 EGYGPLKAHP 340 FFESVTWENL350 HQQTPPKLT
|
|||||
|
|
LEU88
3.054
GLY89
2.311
GLU90
3.091
GLY91
2.580
SER92
2.428
PHE93
4.425
SER94
1.934
THR95
4.424
VAL96
2.515
ALA109
3.050
LYS111
1.909
GLU130
4.628
VAL143
2.670
|
|||||
| PDB ID: 4RRV Crystal structure of PDK1 in complex with ATP and PIFtide | ||||||
| Method | X-ray diffraction | Resolution | 1.41 Å | Mutation | Yes | [4] |
| 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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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
3.045
GLY89
2.187
GLU90
3.087
GLY91
2.614
SER92
1.976
PHE93
4.313
SER94
2.044
THR95
4.383
VAL96
2.563
ALA109
3.024
LYS111
2.512
VAL143
2.779
LEU159
2.781
|
|||||
| PDB ID: 4AW0 Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket | ||||||
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
3.051
GLY89
2.815
GLU90
3.674
GLY91
2.638
SER92
2.075
PHE93
4.144
SER94
1.794
THR95
4.809
VAL96
2.683
ALA109
2.920
LYS111
2.460
VAL143
2.715
LEU159
2.796
|
|||||
| PDB ID: 4RQV Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RS2 | ||||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | Yes | [4] |
| 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 .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
3.068
GLY89
2.070
GLU90
3.174
GLY91
2.653
SER92
2.039
PHE93
4.545
SER94
1.944
THR95
4.207
VAL96
2.664
ALA109
2.964
LYS111
2.892
VAL143
2.710
LEU159
2.821
|
|||||
| PDB ID: 4RQK Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RS1 | ||||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | Yes | [4] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
3.031
GLY89
2.121
GLU90
3.142
GLY91
2.542
SER92
2.134
PHE93
4.257
SER94
1.855
THR95
4.152
VAL96
2.654
ALA109
3.000
LYS111
2.499
VAL143
2.723
LEU159
2.733
|
|||||
| PDB ID: 4AW1 Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the PIF-Pocket | ||||||
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ATP or .ATP2 or .ATP3 or :3ATP;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:113 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:205 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
2.966
GLY89
2.434
GLU90
3.789
GLY91
2.611
SER92
2.219
PHE93
3.466
SER94
2.365
VAL96
2.298
ALA109
2.814
LYS111
2.024
LEU113
4.896
VAL143
2.716
LEU159
2.663
|
|||||
| PDB ID: 4A07 Human PDK1 Kinase Domain in Complex with Allosteric Activator PS171 Bound to the PIF-Pocket | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [6] |
| 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 .ATP or .ATP2 or .ATP3 or :3ATP;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: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:165 or .A:166 or .A:207 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
2.895
GLY89
2.739
GLU90
3.941
GLY91
2.580
SER92
2.339
PHE93
3.947
SER94
2.090
THR95
4.609
VAL96
2.497
ALA109
2.980
LYS111
2.385
VAL143
2.707
|
|||||
| PDB ID: 4CT1 Human PDK1-PKCzeta Kinase Chimera in Complex with Allosteric Compound PS315 Bound to the PIF-Pocket | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [3] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
|
LEU88
3.311
GLY89
2.307
GLU90
3.075
GLY91
2.613
SER92
2.618
PHE93
4.377
SER94
1.998
THR95
4.505
VAL96
2.610
ALA109
2.926
LYS111
3.474
VAL143
2.793
|
|||||
| PDB ID: 3HRF Crystal structure of Human PDK1 kinase domain in complex with an allosteric activator bound to the PIF-pocket | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [7] |
| 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 .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
|
LEU88
4.070
GLY89
3.363
GLU90
3.774
GLY91
3.267
SER92
2.448
PHE93
4.885
SER94
2.449
THR95
4.519
VAL96
3.343
ALA109
3.576
LYS111
3.196
|
|||||
| PDB ID: 3HRC Crystal structure of a mutant of human PDK1 Kinase domain in complex with ATP | ||||||
| Method | X-ray diffraction | Resolution | 1.91 Å | Mutation | Yes | [7] |
| PDB Sequence |
KKRPEDFKFG
85 KILGEGSFST95 VVLARELATS105 REYAIKILEK115 RHIIKENKVP125 YVTRERDVMS 135 RLDHPFFVKL145 YFTFQDDEKL155 YFGLSYAKNG165 ELLKYIRKIG175 SFDETCTRFY 185 TAEIVSALEY195 LHGKGIIHRD205 LKPENILLNE215 DMHIQITDFG225 TAKVLSPARA 239 NFVGTAQYVS250 PELLTEKSAC260 KSSDLWALGC270 IIYQLVAGLP280 PFRAGNEGLI 290 FAKIIKLEYD300 FPEKFFPKAR310 DLVEKLLVLD320 ATKRLGCEEM330 EGYGPLKAHP 340 FFESVTWENL350 HQQTPPKLT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
|
LEU88
3.942
GLY89
3.441
GLU90
3.786
GLY91
3.382
SER92
2.787
PHE93
4.708
SER94
2.689
THR95
4.629
VAL96
3.341
ALA109
3.583
LYS111
2.755
|
|||||
| PDB ID: 4A06 Human PDK1 Kinase Domain in Complex with Allosteric Activator PS114 Bound to the PIF-Pocket | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [6] |
| 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 .ATP or .ATP2 or .ATP3 or :3ATP;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: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:166 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
|
LEU88
3.958
GLY89
3.171
GLU90
3.931
GLY91
3.091
SER92
2.635
PHE93
3.720
SER94
2.626
THR95
4.285
VAL96
3.226
ALA109
3.669
LYS111
3.679
|
|||||
| PDB ID: 5LVP Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | Yes | [1] |
| PDB Sequence |
RKKRPEDFKF
84 GKILGEGSFS94 TVVLARELAT104 SREYAIKILE114 KRHIIKENKV124 PYVTRERDVM 134 SRLDHPFFVK144 LYFTFQDDEK154 LYFGLSYAKN164 GELLKYIRKI174 GSFDETCTRF 184 YTAEIVSALE194 YLHGKGIIHR204 DLKPENILLN214 EDMHIQITDF224 GTAKVLNFVG 244 TAQYVSPELL254 TEKSACKSSD264 LWALGCIIYQ274 LVAGLPPFRA284 GNEGLIFAKI 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 .ATP or .ATP2 or .ATP3 or :3ATP;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:143 or .A:159 or .A:160 or .A:161 or .A:162 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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| PDB ID: 4XX9 Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RF4 | ||||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [8] |
| 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 .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
3.021
GLY89
2.090
GLU90
3.144
GLY91
2.619
SER92
1.889
PHE93
4.503
SER94
1.892
THR95
4.214
VAL96
2.720
ALA109
2.997
LYS111
2.369
VAL143
2.745
LEU159
2.794
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| PDB ID: 5MRD Human PDK1-PKCiota Kinase Chimera in Complex with Allosteric Compound PS267 Bound to the PIF-Pocket | ||||||
| Method | X-ray diffraction | Resolution | 1.41 Å | Mutation | Yes | [9] |
| 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
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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 .ATP or .ATP2 or .ATP3 or :3ATP;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:95 or .A:96 or .A:109 or .A:111 or .A:126 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: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
2.681
GLY89
1.763
GLU90
2.912
GLY91
3.721
SER92
3.718
SER94
2.481
THR95
4.664
VAL96
2.512
ALA109
3.169
LYS111
2.020
TYR126
3.060
VAL143
3.121
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| PDB ID: 2BIY Structure of PDK1-S241A mutant kinase domain | ||||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | Yes | [10] |
| PDB Sequence |
PQPRKKRPED
81 FKFGKILGEG91 SFSTVVLARE101 LATSREYAIK111 ILEKRHIIKE121 NKVPYVTRER 131 DVMSRLDHPF141 FVKLYFTFQD151 DEKLYFGLSY161 AKNGELLKYI171 RKIGSFDETC 181 TRFYTAEIVS191 ALEYLHGKGI201 IHRDLKPENI211 LLNEDMHIQI221 TDFGTAKVLS 231 PESKQARANA241 FVGTAQYVSP251 ELLTEKSACK261 SSDLWALGCI271 IYQLVAGLPP 281 FRAGNEYLIF291 QKIIKLEYDF301 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 .ATP or .ATP2 or .ATP3 or :3ATP;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: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:166 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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| PDB ID: 1H1W High resolution crystal structure of the human PDK1 catalytic domain | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [11] |
| 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
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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 .ATP or .ATP2 or .ATP3 or :3ATP;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: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: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
|
LEU88
3.784
GLY89
3.162
GLU90
3.705
GLY91
3.226
SER92
2.944
PHE93
4.904
SER94
2.584
THR95
4.152
VAL96
3.439
ALA109
3.612
LYS111
2.856
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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 | 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 3 | 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 4 | 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 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 | 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 7 | Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1. Nat Chem Biol. 2009 Oct;5(10):758-64. | ||||
| REF 8 | Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem. 2015 Oct 22;58(20):8285-8291. | ||||
| REF 9 | 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 10 | Role of T-loop phosphorylation in PDK1 activation, stability, and substrate binding. J Biol Chem. 2005 May 13;280(19):18797-802. | ||||
| REF 11 | High resolution crystal structure of the human PDK1 catalytic domain defines the regulatory phosphopeptide docking site. EMBO J. 2002 Aug 15;21(16):4219-28. | ||||
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