Structure of PDB 7ebh Chain A Binding Site BS01

Receptor Information
>7ebh Chain A (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLAN
IMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFT
DALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRI
SIRMLINQHTLIFDGPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMAS
PDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLI
LPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPGYGLPIS
RLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY
Ligand information
Ligand IDJ0F
InChIInChI=1S/C10H12BrN3/c1-3-4-8-9(11)7-5-12-6(2)13-10(7)14-8/h5H,3-4H2,1-2H3,(H,12,13,14)
InChIKeyYMPZAUCKCQGIBE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCc1[nH]c2nc(C)ncc2c1Br
OpenEye OEToolkits 2.0.7CCCc1c(c2cnc(nc2[nH]1)C)Br
FormulaC10 H12 Br N3
Name5-bromanyl-2-methyl-6-propyl-7H-pyrrolo[2,3-d]pyrimidine
ChEMBLCHEMBL4870403
DrugBank
ZINC
PDB chain7ebh Chain A Residue 506 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7ebh Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Resolution1.96 Å
Binding residue
(original residue number in PDB)		N255 M288 D290 V295 L330 L346 T354
Binding residue
(residue number reindexed from 1)		N236 M269 D271 V276 L297 L313 T321
Annotation score1
Enzymatic activity
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:7ebh, PDBe:7ebh, PDBj:7ebh
PDBsum7ebh
PubMed34274549
UniProtQ15119|PDK2_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=PDK2)

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