Structure of PDB 8bay Chain C Binding Site BS02

Receptor Information
>8bay Chain C (length=415) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGCHAYGDQYRATDFVVPGPGKV
EITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALS
KGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLID
DMVAQAMKSEGGFIWACKNYDGDVQSDFVAQGYGSLGMMTSVLVCPDGKT
VEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKEL
AFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLG
ENLKIKLAQAKLLEH
Ligand information
Ligand IDQDC
InChIInChI=1S/C9H14O5/c1-2-3-4-6(5-7(10)11)8(12)9(13)14/h6H,2-5H2,1H3,(H,10,11)(H,13,14)/t6-/m1/s1
InChIKeyRVKQLIHFWCFUHE-ZCFIWIBFSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCC[C@H](CC(O)=O)C(=O)C(O)=O
OpenEye OEToolkits 3.1.0.0CCCCC(CC(=O)O)C(=O)C(=O)O
OpenEye OEToolkits 3.1.0.0CCCC[C@H](CC(=O)O)C(=O)C(=O)O
CACTVS 3.385CCCC[CH](CC(O)=O)C(=O)C(O)=O
FormulaC9 H14 O5
Name(R)-3-butyl-2-oxopentanedioic acid;
(3~{R})-3-butyl-2-oxidanylidene-pentanedioic acid
ChEMBL
DrugBank
ZINC
PDB chain8bay Chain C Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8bay Natural and synthetic 2-oxoglutarate derivatives are substrates for oncogenic variants of human isocitrate dehydrogenase 1 and 2.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		T77 S94 N96 R109 Y139 D275
Binding residue
(residue number reindexed from 1)		T75 S92 N94 R107 Y137 D273
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8bay, PDBe:8bay, PDBj:8bay
PDBsum8bay
PubMed36621625
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

[Back to BioLiP]