Structure of PDB 2zdx Chain A Binding Site BS01

Receptor Information
>2zdx Chain A (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANIL
KEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDT
LIKVRNRHHNVVPTMAQGIIEYNQNLQYFLDRFYMNRISTRMLMNQHILI
FSDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQ
VNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVI
VVLGKEDLTIKISDRGGGVPLRIIDRLFSYTFGYGLPISRLYAKYFQGDL
NLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKH
Ligand information
Ligand IDP4A
InChIInChI=1S/C17H16N2O3/c1-10-16(11-3-6-13(22-2)7-4-11)17(19-18-10)14-8-5-12(20)9-15(14)21/h3-9,20-21H,1-2H3,(H,18,19)
InChIKeyGSBFARPNIZUMHA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1ccc(cc1)c2c(C)[nH]nc2c3ccc(O)cc3O
ACDLabs 10.04Oc3ccc(c2nnc(c2c1ccc(OC)cc1)C)c(O)c3
OpenEye OEToolkits 1.5.0Cc1c(c(n[nH]1)c2ccc(cc2O)O)c3ccc(cc3)OC
FormulaC17 H16 N2 O3
Name4-[4-(4-methoxyphenyl)-5-methyl-1H-pyrazol-3-yl]benzene-1,3-diol;
3-(2,4-dihydroxyphenyl)-4-(4-methoxyphenyl)-5-methyl-1h-pyrazole
ChEMBLCHEMBL192894
DrugBankDB08356
ZINCZINC000004641406
PDB chain2zdx Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2zdx Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.
Resolution2.54 Å
Binding residue
(original residue number in PDB)		N258 A262 D293 V298 L306 F330 T358
Binding residue
(residue number reindexed from 1)		N229 A233 D264 V269 L277 F282 T310
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.19,IC50=648uM
Enzymatic activity
Catalytic site (original residue number in PDB) H250 E254 K257 N258
Catalytic site (residue number reindexed from 1) H221 E225 K228 N229
Enzyme Commision number 2.7.11.2: [pyruvate dehydrogenase (acetyl-transferring)] kinase.
Gene Ontology
Molecular Function
GO:0004672 protein 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:0006885 regulation of pH
GO:0008286 insulin receptor signaling pathway
GO:0009267 cellular response to starvation
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate
GO:0010565 regulation of cellular ketone metabolic process
GO:0010906 regulation of glucose metabolic process
GO:0016310 phosphorylation
GO:0042304 regulation of fatty acid biosynthetic process
GO:0042593 glucose homeostasis
GO:0042594 response to starvation
GO:0045124 regulation of bone resorption
GO:0046320 regulation of fatty acid oxidation
GO:0071398 cellular response to fatty acid
GO:0072593 reactive oxygen species metabolic process
GO:2000811 negative regulation of anoikis
Cellular Component
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:2zdx, PDBe:2zdx, PDBj:2zdx
PDBsum2zdx
PubMed21904029
UniProtQ16654|PDK4_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (Gene Name=PDK4)

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