Structure of PDB 5m4k Chain A Binding Site BS02

Receptor Information
>5m4k Chain A (length=336) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSAPKYIEHFSKFSPSPLSMKQFLDFNACEKTSFTFLRQELPVRLANIMK
EINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDAL
VTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIR
MLINQHTLIFDPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLE
IQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPI
KVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPYGLPISRLYAK
YFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY
Ligand information
Ligand ID7F9
InChIInChI=1S/C18H20N2O5/c1-3-19-17(23)11-20(12-4-7-14(25-2)8-5-12)18(24)15-9-6-13(21)10-16(15)22/h4-10,21-22H,3,11H2,1-2H3,(H,19,23)
InChIKeyYRTAPVLIGYRBPY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCNC(=O)CN(c1ccc(cc1)OC)C(=O)c2ccc(cc2O)O
CACTVS 3.385CCNC(=O)CN(C(=O)c1ccc(O)cc1O)c2ccc(OC)cc2
FormulaC18 H20 N2 O5
Name~{N}-[2-(ethylamino)-2-oxidanylidene-ethyl]-~{N}-(4-methoxyphenyl)-2,4-bis(oxidanyl)benzamide
ChEMBLCHEMBL4072775
DrugBank
ZINCZINC000584905476
PDB chain5m4k Chain A Residue 402 [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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PDB5m4k Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		N247 R250 A251 D282 V287 T346
Binding residue
(residue number reindexed from 1)		N232 R235 A236 D267 V272 T316
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.66,Ki=2.17uM
BindingDB: IC50=4460nM,Ki=2170nM
Enzymatic activity
Catalytic site (original residue number in PDB) H239 E243 K246 N247
Catalytic site (residue number reindexed from 1) H224 E228 K231 N232
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:5m4k, PDBe:5m4k, PDBj:5m4k
PDBsum5m4k
PubMed28199108
UniProtQ15119|PDK2_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=PDK2)

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