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 | DTD | Ligand Info | |||
| Canonical SMILES | C1C(C(CSS1)O)O | ||||
| InChI | 1S/C4H8O2S2/c5-3-1-7-8-2-4(3)6/h3-6H,1-2H2/t3-,4-/m0/s1 | ||||
| InChIKey | YPGMOWHXEQDBBV-IMJSIDKUSA-N | ||||
| PubChem Compound ID | 439407 | ||||
| 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
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| 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
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| 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
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| PDB ID: 5LVM Human PDK1 Kinase Domain in Complex with Adenine Bound to the ATP-Binding Site | ||||||
| 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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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 #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5LVN Human PDK1 Kinase Domain in Complex with Adenosine Bound to the ATP-Binding Site | ||||||
| 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 .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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| PDB ID: 5LVL Human PDK1 Kinase Domain in Complex with Compound PS653 Bound to the ATP-Binding Site | ||||||
| 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 .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 #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| 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 | [4] |
| 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 .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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| 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
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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 #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 | 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 | 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. | ||||
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