Structure of PDB 5yfn Chain A Binding Site BS01

Receptor Information
>5yfn Chain A (length=418) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLYFQSMMSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYD
LGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWK
SPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATD
FVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFA
HSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQK
IWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTS
VLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHR
AKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLN
TFEFMDKLGENLKIKLAQ
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5yfn 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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PDB5yfn Human isocitrate dehydrogenase 1 bound with isocitrate
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D275 D279
Binding residue
(residue number reindexed from 1)		D282 D286
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:5yfn, PDBe:5yfn, PDBj:5yfn
PDBsum5yfn
PubMed
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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