Structure of PDB 5m4p Chain A Binding Site BS01

Receptor Information
>5m4p Chain A (length=343) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSAPKYIEHFSKFSPSPLSMKQFLDFGSNACEKTSFTFLRQELPVRLANI
MKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTD
ALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRIS
IRMLINQHTLIFDPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPD
LEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILP
PIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPLAGFGYGLP
ISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY
Ligand information
Ligand ID7FE
InChIInChI=1S/C30H29ClN4O3/c1-20-17-32-30(31)33-28(20)23-8-10-24(11-9-23)35(29(38)26-13-12-25(36)16-27(26)37)19-22-6-4-21(5-7-22)18-34-14-2-3-15-34/h4-13,16-17,36-37H,2-3,14-15,18-19H2,1H3
InChIKeyWJKWCGYIPOTSBR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cnc(Cl)nc1c2ccc(cc2)N(Cc3ccc(CN4CCCC4)cc3)C(=O)c5ccc(O)cc5O
OpenEye OEToolkits 2.0.6Cc1cnc(nc1c2ccc(cc2)N(Cc3ccc(cc3)CN4CCCC4)C(=O)c5ccc(cc5O)O)Cl
FormulaC30 H29 Cl N4 O3
Name~{N}-[4-(2-chloranyl-5-methyl-pyrimidin-4-yl)phenyl]-2,4-bis(oxidanyl)-~{N}-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]benzamide
ChEMBLCHEMBL3727843
DrugBank
ZINCZINC000584905463
PDB chain5m4p Chain A Residue 401 [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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PDB5m4p Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K246 N247 R250 A251 D282 G284 G286 V287 T346
Binding residue
(residue number reindexed from 1)		K233 N234 R237 A238 D269 G271 G273 V274 T323
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H239 E243 K246 N247
Catalytic site (residue number reindexed from 1) H226 E230 K233 N234
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
GO:0042803 protein homodimerization activity
Biological Process
GO:0006006 glucose metabolic process
GO:0006111 regulation of gluconeogenesis
GO:0006885 regulation of pH
GO:0008286 insulin receptor signaling pathway
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:0031670 cellular response to nutrient
GO:0034614 cellular response to reactive oxygen species
GO:0042593 glucose homeostasis
GO:0050848 regulation of calcium-mediated signaling
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0045254 pyruvate dehydrogenase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m4p, PDBe:5m4p, PDBj:5m4p
PDBsum5m4p
PubMed28199108
UniProtQ15119|PDK2_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=PDK2)

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