Structure of PDB 5m4k Chain A Binding Site BS01

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 IDTF3
InChIInChI=1S/C20H25ClN2O2/c1-14(2)17-6-3-15(4-7-17)13-25-19-8-5-16(11-18(19)21)12-20(24)23-10-9-22/h3-8,11,14H,9-10,12-13,22H2,1-2H3,(H,23,24)
InChIKeyDFXJYVQAAFOZDP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc2cc(ccc2OCc1ccc(cc1)C(C)C)CC(=O)NCCN
OpenEye OEToolkits 1.5.0CC(C)c1ccc(cc1)COc2ccc(cc2Cl)CC(=O)NCCN
CACTVS 3.341CC(C)c1ccc(COc2ccc(CC(=O)NCCN)cc2Cl)cc1
FormulaC20 H25 Cl N2 O2
NameN-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE
ChEMBLCHEMBL1236255
DrugBankDB08610
ZINCZINC000016051834
PDB chain5m4k Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		R66 V67 Y129 N142 I143
Binding residue
(residue number reindexed from 1)		R58 V59 Y121 N134 I135
Annotation score1
Binding affinityBindingDB: IC50=2000nM
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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