Structure of PDB 5yzi Chain A Binding Site BS01

Receptor Information
>5yzi Chain A (length=409) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIQGGSVVEMQGDEMTRIIWELIKEKLILPYVELDLHSYDLGIENRDATN
DQVTKDAAEAIKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNIL
GGTVFREAIICKNIPRLVTGWVKPIIIGRHAYGDQYRATDFVVPGPGKVE
ITYTPKDGTQKVTYMVHDFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSK
GWPLYLSTKNTILKKYDGRFKDIFQEIYDKKYKSQFEAQKICYEHRLIDD
MVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLICPDGKTV
EAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWSRGLAHRAKLDNNTELS
FFAKALEDVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGE
NLKAKLAQA
Ligand information
Ligand IDCD
InChIInChI=1S/Cd/q+2
InChIKeyWLZRMCYVCSSEQC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Cd++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Cd+2]
FormulaCd
NameCADMIUM ION
ChEMBL
DrugBank
ZINC
PDB chain5yzi Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yzi NADP+-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione.
Resolution2.519 Å
Binding residue
(original residue number in PDB)		D275 D279
Binding residue
(residue number reindexed from 1)		D272 D276
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: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: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: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:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yzi, PDBe:5yzi, PDBj:5yzi
PDBsum5yzi
PubMed29923039
UniProtO88844|IDHC_MOUSE Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=Idh1)

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