Structure of PDB 7pjn Chain D Binding Site BS01

Receptor Information
>7pjn Chain D (length=408) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDA
TNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRN
ILGGTVFREAIICKNIPRLVSGWVKPIIIGCHAYGDQYRATDFVVPGPGK
VEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMAL
SKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLI
DDMVAQAMKSEGGFIWACKNYDSDFVAQGYGSLGMMTSVLVCPDGKTVEA
EAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFF
ANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENL
KIKLAQAK
Ligand information
Ligand ID7SU
InChIInChI=1S/C25H18Cl3FN2O4/c1-12-11-31(17-6-4-5-13(19(12)17)7-8-18(32)33)24(34)21-22(30-35-23(21)25(2,3)29)20-15(27)9-14(26)10-16(20)28/h4-11H,1-3H3,(H,32,33)/b8-7+
InChIKeyBOOMBLZEOHXPPX-BQYQJAHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cn(c2c1c(ccc2)C=CC(=O)O)C(=O)c3c(noc3C(C)(C)F)c4c(cc(cc4Cl)Cl)Cl
CACTVS 3.385Cc1cn(C(=O)c2c(onc2c3c(Cl)cc(Cl)cc3Cl)C(C)(C)F)c4cccc(C=CC(O)=O)c14
CACTVS 3.385Cc1cn(C(=O)c2c(onc2c3c(Cl)cc(Cl)cc3Cl)C(C)(C)F)c4cccc(\C=C\C(O)=O)c14
OpenEye OEToolkits 2.0.7Cc1cn(c2c1c(ccc2)/C=C/C(=O)O)C(=O)c3c(noc3C(C)(C)F)c4c(cc(cc4Cl)Cl)Cl
FormulaC25 H18 Cl3 F N2 O4
Name(E)-3-(1-(5-(2-fluoropropan-2-yl)-3-(2,4,6-trichlorophenyl)isoxazole-4-carbonyl)-3-methyl-1H-indol-4-yl)acrylic acid ;
(2E)-3-(1-{[5-(2-Fluoropropan-2-yl)-3-(2,4,6-trichlorophenyl)-1,2-oxazol-4-yl]carbonyl}-3-methyl-1H-indol-4-yl)prop-2-enoic acid
ChEMBLCHEMBL4651002
DrugBank
ZINC
PDB chain7pjn Chain D Residue 601 [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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PDB7pjn Resistance to the isocitrate dehydrogenase 1 mutant inhibitor ivosidenib can be overcome by alternative dimer-interface binding inhibitors.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		A111 R119 L120 W124 I130 M259 W267 V281
Binding residue
(residue number reindexed from 1)		A110 R118 L119 W123 I129 M258 W266 V276
Annotation score1
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:7pjn, PDBe:7pjn, PDBj:7pjn
PDBsum7pjn
PubMed35970853
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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