Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T99029 | Target Info | |||
| Target Name | Pyruvate dehydrogenase kinase 3 (PDHK3) | ||||
| Synonyms | Pyruvate dehydrogenase kinase isoform 3; PDK3 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | PDK3 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Dihydrolipoic acid | Ligand Info | |||
| Canonical SMILES | C(CCC(=O)O)CC(CCS)S | ||||
| InChI | 1S/C8H16O2S2/c9-8(10)4-2-1-3-7(12)5-6-11/h7,11-12H,1-6H2,(H,9,10) | ||||
| InChIKey | IZFHEQBZOYJLPK-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 421 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1Y8O Crystal structure of the PDK3-L2 complex | ||||||
| Method | X-ray diffraction | Resolution | 2.48 Å | Mutation | No | [1] |
| PDB Sequence |
PKQIERYSRF
22 SPSPLSIKQF32 LDFGRDNACE42 KTSYMFLRKE52 LPVRLANTMR62 EVNLLPDNLL 72 NRPSVGLVQS82 WYMQSFLELL92 EYENKSPEDP102 QVLDNFLQVL112 IKVRNRHNDV 122 VPTMAQGVIE132 YKEKFGFDPF142 ISTNIQYFLD152 RFYTNRISFR162 MLINQHTLLF 172 GGDTNPVHPK182 HIGSIDPTCN192 VADVVKDAYE202 TAKMLCEQYY212 LVAPELEVEE 222 FNAKAPDKPI232 QVVYVPSHLF242 HMLFELFKNS252 MRATVELYED262 RKEGYPAVKT 272 LVTLGKEDLS282 IKISDLGGGV292 PLRKIDRLFN302 YMYSPLFGYG327 LPISRLYARY 337 FQGDLKLYSM347 EGVGTDAVIY357 LKALSSESFE367 RLPVFNKSAW377 RHYKTTPEAD 387 DWSNPSSEPR397 DASK
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| PDB ID: 2PNR Crystal Structure of the asymmetric Pdk3-l2 Complex | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [2] |
| PDB Sequence |
PKQIERYSRF
22 SPSPLSIKQF32 LDFGRDNACE42 KTSYMFLRKE52 LPVRLANTMR62 EVNLLPDNLL 72 NRPSVGLVQS82 WYMQSFLELL92 EYENKSPEDP102 QVLDNFLQVL112 IKVRNRHNDV 122 VPTMAQGVIE132 YKEKFGFDPF142 ISTNIQYFLD152 RFYTNRISFR162 MLINQHTLLF 172 GGDTNPVHPK182 HIGSIDPTCN192 VADVVKDAYE202 TAKMLCEQYY212 LVAPELEVEE 222 FNAKAPDKPI232 QVVYVPSHLF242 HMLFELFKNS252 MRATVELYED262 RKEGYPAVKT 272 LVTLGKEDLS282 IKISDLGGGV292 PLRKIDRLFN302 YAAPLAGFGY326 GLPISRLYAR 336 YFQGDLKLYS346 MEGVGTDAVI356 YLKALSSESF366 ERLPVFNKSA376 WRHYKTTPEA 386 DDWSNPSSEP396 RDAS
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| PDB ID: 1Y8N Crystal structure of the PDK3-L2 complex | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [1] |
| PDB Sequence |
PKQIERYSRF
22 SPSPLSIKQF32 LDFGRDNACE42 KTSYMFLRKE52 LPVRLANTMR62 EVNLLPDNLL 72 NRPSVGLVQS82 WYMQSFLELL92 EYENKSPEDP102 QVLDNFLQVL112 IKVRNRHNDV 122 VPTMAQGVIE132 YKEKFGFDPF142 ISTNIQYFLD152 RFYTNRISFR162 MLINQHTLLF 172 GGDTNPVHPK182 HIGSIDPTCN192 VADVVKDAYE202 TAKMLCEQYY212 LVAPELEVEE 222 FNAKAPDKPI232 QVVYVPSHLF242 HMLFELFKNS252 MRATVELYED262 RKEGYPAVKT 272 LVTLGKEDLS282 IKISDLGGGV292 PLRKIDRLFN302 YMYSPLFGYG327 LPISRLYARY 337 FQGDLKLYSM347 EGVGTDAVIY357 LKALSSESFE367 RLPVFNKSAW377 RHYKTTPEAD 387 DWSNPSSEPR397 DASK
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| PDB ID: 2Q8I Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [3] |
| PDB Sequence |
PKQIERYSRF
22 SPSPLSIKQF32 LDFGRDNACE42 KTSYMFLRKE52 LPVRLANTMR62 EVNLLPDNLL 72 NRPSVGLVQS82 WYMQSFLELL92 EYENKSPEDP102 QVLDNFLQVL112 IKVRNRHNDV 122 VPTMAQGVIE132 YKEKFGFDPF142 ISTNIQYFLD152 RFYTNRISFR162 MLINQHTLLF 172 GTNPVHPKHI184 GSIDPTCNVA194 DVVKDAYETA204 KMLCEQYYLV214 APELEVEEFN 224 AKAPDKPIQV234 VYVPSHLFHM244 LFELFKNSMR254 ATVELYEDRK264 EGYPAVKTLV 274 TLGKEDLSIK284 ISDLGGGVPL294 RKIDRLFNYM304 YSGYGLPISR332 LYARYFQGDL 342 KLYSMEGVGT352 DAVIYLKALS362 SESFERLPVF372 NKSAWRHYKT382 TPEADDWSNP 392 SSEPRDASK
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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 .RED or .RED2 or .RED3 or :3RED;style chemicals stick;color identity;select .A:27 or .A:31 or .A:32 or .A:35 or .A:44 or .A:45 or .A:48 or .A:49 or .A:164 or .A:167 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 1Y8P Crystal structure of the PDK3-L2 complex | ||||||
| Method | X-ray diffraction | Resolution | 2.63 Å | Mutation | No | [1] |
| PDB Sequence |
VPKQIERYSR
21 FSPSPLSIKQ31 FLDFGRDNAC41 EKTSYMFLRK51 ELPVRLANTM61 REVNLLPDNL 71 LNRPSVGLVQ81 SWYMQSFLEL91 LEYENKSPED101 PQVLDNFLQV111 LIKVRNRHND 121 VVPTMAQGVI131 EYKEKFGFDP141 FISTNIQYFL151 DRFYTNRISF161 RMLINQHTLL 171 FGGDTNPVHP181 KHIGSIDPTC191 NVADVVKDAY201 ETAKMLCEQY211 YLVAPELEVE 221 EFNAKAPDKP231 IQVVYVPSHL241 FHMLFELFKN251 SMRATVELYE261 DRKEGYPAVK 271 TLVTLGKEDL281 SIKISDLGGG291 VPLRKIDRLF301 NYMYSTAPRP320 LAGFGYGLPI 330 SRLYARYFQG340 DLKLYSMEGV350 GTDAVIYLKA360 LSSESFERLP370 VFNKSAWRHY 380 KTTPEADDWS390 NPSSEPRDAS400 K
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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 .RED or .RED2 or .RED3 or :3RED;style chemicals stick;color identity;select .A:27 or .A:31 or .A:32 or .A:35 or .A:44 or .A:45 or .A:48 or .A:49 or .A:164 or .A:167; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex. EMBO J. 2005 May 18;24(10):1763-74. | ||||
| REF 2 | Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications. J Mol Biol. 2007 Jul 13;370(3):407-16. | ||||
| REF 3 | Distinct structural mechanisms for inhibition of pyruvate dehydrogenase kinase isoforms by AZD7545, dichloroacetate, and radicicol. Structure. 2007 Aug;15(8):992-1004. | ||||
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