Structure of PDB 6io0 Chain A Binding Site BS01

Receptor Information
>6io0 Chain A (length=400) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGCHRATDFVVPGPGKVEITYTP
SDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLY
LSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQA
MKSEGGFIWACKVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVT
RHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVS
IETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK
Ligand information
Ligand IDAOU
InChIInChI=1S/C25H20Cl2N2O4/c1-13(2)25-21(22(28-33-25)20-17(26)8-5-9-18(20)27)24(32)16-12-29(3)23-14(10-11-19(30)31)6-4-7-15(16)23/h4-13H,1-3H3,(H,30,31)/b11-10+
InChIKeyUIMYWZDHAJEOJS-ZHACJKMWSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c4cc(c(c3noc(c3C(c1cn(c2c1cccc2[C@H]=CC(O)=O)C)=O)C(C)C)c(c4)Cl)Cl
CACTVS 3.385CC(C)c1onc(c2c(Cl)cccc2Cl)c1C(=O)c3cn(C)c4c(cccc34)C=CC(O)=O
OpenEye OEToolkits 2.0.6CC(C)c1c(c(no1)c2c(cccc2Cl)Cl)C(=O)c3cn(c4c3cccc4C=CC(=O)O)C
OpenEye OEToolkits 2.0.6CC(C)c1c(c(no1)c2c(cccc2Cl)Cl)C(=O)c3cn(c4c3cccc4/C=C/C(=O)O)C
CACTVS 3.385CC(C)c1onc(c2c(Cl)cccc2Cl)c1C(=O)c3cn(C)c4c(cccc34)/C=C/C(O)=O
FormulaC25 H20 Cl2 N2 O4
Name(2E)-3-{3-[3-(2,6-dichlorophenyl)-5-(propan-2-yl)-1,2-oxazole-4-carbonyl]-1-methyl-1H-indol-7-yl}prop-2-enoic acid
ChEMBL
DrugBank
ZINC
PDB chain6io0 Chain A Residue 501 [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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PDB6io0 A Potent Blood-Brain Barrier-Permeable Mutant IDH1 Inhibitor Suppresses the Growth of Glioblastoma with IDH1 Mutation in a Patient-Derived Orthotopic Xenograft Model.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R119 L120 W124 I130 M259 W267
Binding residue
(residue number reindexed from 1)		R117 L118 W122 I128 M251 W259
Annotation score1
Binding affinityMOAD: ic50=130nM
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:6io0, PDBe:6io0, PDBj:6io0
PDBsum6io0
PubMed31727689
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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