Structure of PDB 8vha Chain D Binding Site BS01

Receptor Information
>8vha Chain D (length=412) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDA
TNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRN
ILGGTVFREAIICKNIPRLVSGWVKPIIIGQHAYGDQYRATDFVVPGPGK
VEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMAL
SKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLI
DDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGK
TVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKE
LAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKL
GENLKIKLAQAK
Ligand information
Ligand IDEE1
InChIInChI=1S/C26H34N7O22P3/c27-21-15-23(30-7-29-21)33(8-31-15)25-20(54-56(43,44)45)18(38)13(53-25)6-51-58(48,49)55-57(46,47)50-5-12-17(37)19(39)24(52-12)32-2-1-9(11(4-32)22(28)40)10(3-14(34)35)16(36)26(41)42/h1-2,4,7-10,12-13,17-20,24-25,37-39H,3,5-6H2,(H2,28,40)(H,34,35)(H,41,42)(H,46,47)(H,48,49)(H2,27,29,30)(H2,43,44,45)/t9-,10-,12+,13+,17+,18+,19+,20+,24+,25+/m0/s1
InChIKeyWSGZIHXYYXDDDT-PJNAXEGASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CC(C(=C5)C(=O)N)C(CC(=O)O)C(=O)C(=O)O)O)O)O)OP(=O)(O)O)N
CACTVS 3.385NC(=O)C1=CN(C=C[C@H]1[C@H](CC(O)=O)C(=O)C(O)=O)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=C[C@H](C(=C5)C(=O)N)[C@H](CC(=O)O)C(=O)C(=O)O)O)O)O)OP(=O)(O)O)N
CACTVS 3.385NC(=O)C1=CN(C=C[CH]1[CH](CC(O)=O)C(=O)C(O)=O)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC26 H34 N7 O22 P3
Name(3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid;
NADPH with ketoglutarate adduct
ChEMBL
DrugBank
ZINC
PDB chain8vha Chain C Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8vha Active site remodeling in tumor-relevant IDH1 mutants drive distinct kinetic features and possible resistance mechanisms
Resolution2.28 Å
Binding residue
(original residue number in PDB)
K212 D253 K260
Binding residue
(residue number reindexed from 1)
K211 D252 K259
Annotation score3
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:8vha, PDBe:8vha, PDBj:8vha
PDBsum8vha
PubMed38710674
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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