Structure of PDB 4xs3 Chain B Binding Site BS02

Receptor Information
>4xs3 Chain B (length=381) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATN
DQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNIL
GGTVFREAIICKNIPRVKPIIIGHHATDFVVPGPGKVEITYTPSDGTQKV
TYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTI
LKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGF
IWACSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIAS
IFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKG
LPNVQRSDYLNTFEFMDKLGENLKIKLAQAK
Ligand information
Ligand ID42W
InChIInChI=1S/C17H15N3O2S/c1-19-16(22)14(18-17(19)23)9-13-7-8-15(21)20(11-13)10-12-5-3-2-4-6-12/h2-9,11H,10H2,1H3,(H,18,23)/b14-9+
InChIKeyORESZEYKAHLKRD-NTEUORMPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=S)N/C(=C/C2=CN(Cc3ccccc3)C(=O)C=C2)C1=O
OpenEye OEToolkits 2.0.4CN1C(=O)C(=CC2=CN(C(=O)C=C2)Cc3ccccc3)NC1=S
ACDLabs 12.01C=2C(N(Cc1ccccc1)C=C(C=2)\C=C3\NC(N(C)C3=O)=S)=O
CACTVS 3.385CN1C(=S)NC(=CC2=CN(Cc3ccccc3)C(=O)C=C2)C1=O
FormulaC17 H15 N3 O2 S
Name(E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one;
1-benzyl-5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one
ChEMBLCHEMBL3605388
DrugBank
ZINCZINC000474609270
PDB chain4xs3 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4xs3 Inhibition of Cancer-Associated Mutant Isocitrate Dehydrogenases by 2-Thiohydantoin Compounds.
Resolution3.291 Å
Binding residue
(original residue number in PDB)		T77 K93 S94 G97
Binding residue
(residue number reindexed from 1)		T74 K90 S91 G94
Annotation score1
Binding affinityBindingDB: Ki=32900nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4xs3, PDBe:4xs3, PDBj:4xs3
PDBsum4xs3
PubMed26280302
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

[Back to BioLiP]