Structure of PDB 6o2y Chain A Binding Site BS01

Receptor Information
>6o2y Chain A (length=413) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKV
EITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALS
KGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLID
DMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKT
VEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKEL
AFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLG
ENLKIKLAQAKLE
Ligand information
Ligand IDLJY
InChIInChI=1S/C18H14ClN3O2/c1-24-17-8-15(4-2-11(17)9-20)21-10-13-6-12-7-14(19)3-5-16(12)22-18(13)23/h2-8,21H,10H2,1H3,(H,22,23)
InChIKeyDHTDEOJRSYUVPD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1cc(ccc1C#N)NCC2=Cc3cc(ccc3NC2=O)Cl
CACTVS 3.385COc1cc(NCC2=Cc3cc(Cl)ccc3NC2=O)ccc1C#N
ACDLabs 12.01COc3c(ccc(NCC=2C(Nc1ccc(Cl)cc1C=2)=O)c3)C#N
FormulaC18 H14 Cl N3 O2
Name4-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methoxybenzonitrile
ChEMBLCHEMBL4440107
DrugBank
ZINC
PDB chain6o2y Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6o2y Discovery and Optimization of Quinolinone Derivatives as Potent, Selective, and Orally Bioavailable Mutant Isocitrate Dehydrogenase 1 (mIDH1) Inhibitors.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		R109 A111 I113 R119 W124 I130 W267 D279 V281 Y285
Binding residue
(residue number reindexed from 1)		R107 A109 I111 R117 W122 I128 W265 D277 V279 Y283
Annotation score1
Binding affinityBindingDB: IC50=266nM
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
View graph for
Cellular Component
External links
PDB RCSB:6o2y, PDBe:6o2y, PDBj:6o2y
PDBsum6o2y
PubMed31199148
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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