Structure of PDB 4mpe Chain A Binding Site BS01

Receptor Information
>4mpe Chain A (length=363) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLAGAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRL
ANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQ
FTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLS
RISIRMLINQHTLIFDPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKY
YMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHE
SSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTGYGLP
ISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRH
YQTIQEAGDWCVP
Ligand information
Ligand IDPV8
InChIInChI=1S/C14H13NO5S/c16-11-2-1-9-7-15(8-10(9)5-11)21(19,20)14-4-3-12(17)6-13(14)18/h1-6,16-18H,7-8H2
InChIKeyWRKXOYGLVREKOE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(cc1O)CN(C2)S(=O)(=O)c3ccc(cc3O)O
CACTVS 3.385Oc1ccc(c(O)c1)[S](=O)(=O)N2Cc3ccc(O)cc3C2
ACDLabs 12.01O=S(=O)(c1ccc(O)cc1O)N3Cc2ccc(O)cc2C3
FormulaC14 H13 N O5 S
Name4-[(5-hydroxy-1,3-dihydro-2H-isoindol-2-yl)sulfonyl]benzene-1,3-diol
ChEMBLCHEMBL4062355
DrugBank
ZINCZINC000095920797
PDB chain4mpe Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4mpe Structure-guided Development of Specific Pyruvate Dehydrogenase Kinase Inhibitors Targeting the ATP-binding Pocket.
Resolution1.953 Å
Binding residue
(original residue number in PDB)		N255 R258 A259 E262 D290 G294 V295 T354
Binding residue
(residue number reindexed from 1)		N240 R243 A244 E247 D275 G279 V280 T323
Annotation score1
Binding affinityMOAD: Kd=426nM
PDBbind-CN: -logKd/Ki=6.37,Kd=426nM
BindingDB: Kd=426nM,IC50=570nM
Enzymatic activity
Catalytic site (original residue number in PDB) H247 E251 K254 N255
Catalytic site (residue number reindexed from 1) H232 E236 K239 N240
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:4mpe, PDBe:4mpe, PDBj:4mpe
PDBsum4mpe
PubMed24356970
UniProtQ15119|PDK2_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=PDK2)

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