Structure of PDB 4xrx Chain A Binding Site BS02

Receptor Information
>4xrx Chain A (length=390) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGHHYRATDFVVPGPGKVEITYT
PSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPL
YLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQ
AMKSEGGFIWACKSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQ
ETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMT
KDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK
Ligand information
Ligand ID42V
InChIInChI=1S/C10H9N3O2S/c1-13-9(15)7(12-10(13)16)4-6-2-3-8(14)11-5-6/h2-5H,1H3,(H,11,14)(H,12,16)/b7-4+
InChIKeyIWSWTVREIULVFV-QPJJXVBHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=S)NC(=C/C2=CNC(=O)C=C2)/C1=O
CACTVS 3.385CN1C(=S)NC(=CC2=CNC(=O)C=C2)C1=O
OpenEye OEToolkits 1.9.2CN1C(=O)C(=CC2=CNC(=O)C=C2)NC1=S
OpenEye OEToolkits 1.9.2CN1C(=O)/C(=C\C2=CNC(=O)C=C2)/NC1=S
ACDLabs 12.01S=C2NC(=C\C=1C=CC(=O)NC=1)\C(=O)N2C
FormulaC10 H9 N3 O2 S
Name5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one
ChEMBLCHEMBL3605382
DrugBank
ZINCZINC000263620579
PDB chain4xrx Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xrx Inhibition of Cancer-Associated Mutant Isocitrate Dehydrogenases by 2-Thiohydantoin Compounds.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S94 N96 G97 R100 N101
Binding residue
(residue number reindexed from 1)		S92 N94 G95 R98 N99
Annotation score1
Binding affinityBindingDB: Ki=1200nM
Enzymatic activity
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004450 isocitrate dehydrogenase (NADP+) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0045296 cadherin binding
GO:0046872 metal ion binding
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process
GO:0006103 2-oxoglutarate metabolic process
GO:0006739 NADP metabolic process
GO:0006749 glutathione metabolic process
GO:0006979 response to oxidative stress
GO:0008585 female gonad development
GO:0014070 response to organic cyclic compound
GO:0048545 response to steroid hormone
GO:0060696 regulation of phospholipid catabolic process
GO:0071071 regulation of phospholipid biosynthetic process
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904724 tertiary granule lumen
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4xrx, PDBe:4xrx, PDBj:4xrx
PDBsum4xrx
PubMed26280302
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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