Structure of PDB 8hb9 Chain DDD Binding Site BS01

Receptor Information
>8hb9 Chain DDD (length=399) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRD
ATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIR
NILGGTVFREAIICKNIPRLVSGWVKPIIIGHHATDFVVPGPGKVEITYT
PSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPL
YLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQ
AMKSEGGFIWACKNQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTV
TRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEV
SIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQ
Ligand information
Ligand IDR1R
InChIInChI=1S/C32H49FN7O5S2/c1-22(2)29-20-45-32(42)39(29)30-28(33)17-34-31(36-30)35-23(3)25-7-9-27(10-8-25)38-13-11-26(12-14-38)37-47(43,44)16-15-46-21-24(19-41)18-40(4,5)6/h7-10,17,19,22-24,26,29,37H,11-16,18,20-21H2,1-6H3,(H,34,35,36)/q+1/t23-,24?,29+/m0/s1
InChIKeyLCIIBZXZTLMNNC-QFTSJRPJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)C1COC(=O)N1c2c(cnc(n2)NC(C)c3ccc(cc3)N4CCC(CC4)NS(=O)(=O)CCSCC(C[N+](C)(C)C)C=O)F
CACTVS 3.385CC(C)[C@H]1COC(=O)N1c2nc(N[C@@H](C)c3ccc(cc3)N4CCC(CC4)N[S](=O)(=O)CCSCC(C[N+](C)(C)C)C=O)ncc2F
CACTVS 3.385CC(C)[CH]1COC(=O)N1c2nc(N[CH](C)c3ccc(cc3)N4CCC(CC4)N[S](=O)(=O)CCSCC(C[N+](C)(C)C)C=O)ncc2F
OpenEye OEToolkits 2.0.7C[C@@H](c1ccc(cc1)N2CCC(CC2)NS(=O)(=O)CCSCC(C[N+](C)(C)C)C=O)Nc3ncc(c(n3)N4[C@H](COC4=O)C(C)C)F
FormulaC32 H49 F N7 O5 S2
Name[2-[2-[[1-[4-[(1S)-1-[[5-fluoranyl-4-[(4S)-2-oxidanylidene-4-propan-2-yl-1,3-oxazolidin-3-yl]pyrimidin-2-yl]amino]ethyl]phenyl]piperidin-4-yl]sulfamoyl]ethylsulfanylmethyl]-3-oxidanylidene-propyl]-trimethyl-azanium
ChEMBL
DrugBank
ZINC
PDB chain8hb9 Chain DDD 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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PDB8hb9 Structure-based discovery of IHMT-IDH1-053 as a potent irreversible IDH1 mutant selective inhibitor.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		R109 A111 I113 R119 L120 W124 I128 C269A A282 S287 M291
Binding residue
(residue number reindexed from 1)		R109 A111 I113 R119 L120 W124 I128 C262 A270 S275 M279
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
View graph for
Cellular Component
External links
PDB RCSB:8hb9, PDBe:8hb9, PDBj:8hb9
PDBsum8hb9
PubMed37209613
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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