Structure of PDB 2q8i Chain A Binding Site BS01

Receptor Information
>2q8i Chain A (length=369) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKQIERYSRFSPSPLSIKQFLDFGRDNACEKTSYMFLRKELPVRLANTMR
EVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNFLQVL
IKVRNRHNDVVPTMAQGVIEYKEKFGFDPFISTNIQYFLDRFYTNRISFR
MLINQHTLLFGTNPVHPKHIGSIDPTCNVADVVKDAYETAKMLCEQYYLV
APELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYEDRK
EGYPAVKTLVTLGKEDLSIKISDLGGGVPLRKIDRLFNYMYSGYGLPISR
LYARYFQGDLKLYSMEGVGTDAVIYLKALSSESFERLPVFNKSAWRHYKT
TPEADDWSNPSSEPRDASK
Ligand information
Ligand IDRDC
InChIInChI=1S/C18H17ClO6/c1-9-6-15-14(25-15)5-3-2-4-10(20)7-11-16(18(23)24-9)12(21)8-13(22)17(11)19/h2-5,8-9,14-15,21-22H,6-7H2,1H3/b4-2+,5-3-/t9-,14-,15-/m1/s1
InChIKeyWYZWZEOGROVVHK-GTMNPGAYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1CC2C(O2)C=CC=CC(=O)Cc3c(c(cc(c3Cl)O)O)C(=O)O1
OpenEye OEToolkits 1.5.0C[C@@H]1C[C@@H]2[C@H](O2)\C=C/C=C/C(=O)Cc3c(c(cc(c3Cl)O)O)C(=O)O1
CACTVS 3.341C[C@@H]1C[C@H]2O[C@@H]2\C=C/C=C/C(=O)Cc3c(Cl)c(O)cc(O)c3C(=O)O1
ACDLabs 10.04O=C2C=CC=CC3OC3CC(OC(=O)c1c(O)cc(O)c(Cl)c1C2)C
CACTVS 3.341C[CH]1C[CH]2O[CH]2C=CC=CC(=O)Cc3c(Cl)c(O)cc(O)c3C(=O)O1
FormulaC18 H17 Cl O6
NameRADICICOL;
MONORDEN
ChEMBLCHEMBL414883
DrugBankDB03758
ZINCZINC000013521629
PDB chain2q8i Chain A Residue 408 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2q8i Distinct Structural Mechanisms for Inhibition of Pyruvate Dehydrogenase Kinase Isoforms by AZD7545, Dichloroacetate, and Radicicol.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		N251 A255 D287 V292 L300 L328 T352
Binding residue
(residue number reindexed from 1)		N237 A241 D273 V278 L286 L296 T320
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.40,IC50=400uM
Enzymatic activity
Catalytic site (original residue number in PDB) H243 E247 K250 N251
Catalytic site (residue number reindexed from 1) H229 E233 K236 N237
Enzyme Commision number 2.7.11.2: [pyruvate dehydrogenase (acetyl-transferring)] kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004740 pyruvate dehydrogenase (acetyl-transferring) kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate
GO:0010906 regulation of glucose metabolic process
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0035357 peroxisome proliferator activated receptor signaling pathway
GO:0071333 cellular response to glucose stimulus
GO:0071398 cellular response to fatty acid
GO:0097411 hypoxia-inducible factor-1alpha signaling pathway
GO:2000377 regulation of reactive oxygen species metabolic process
Cellular Component
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2q8i, PDBe:2q8i, PDBj:2q8i
PDBsum2q8i
PubMed17683942
UniProtQ15120|PDK3_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial (Gene Name=PDK3)

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