Structure of PDB 5yvt Chain A Binding Site BS01

Receptor Information
>5yvt Chain A (length=332) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWMI
PSEAKESMDKNKMGLKGPLKTPIAAPSMNLLLRKTFDLYANVRPCVSIEG
YKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEF
AFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYL
DTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANG
VAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACF
ATIKDGKSLTKDLGGNAKCSDFTEEICRRVKD
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 chain5yvt Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yvt Insights into the inhibitory mechanisms of NADH on the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D230 D234
Binding residue
(residue number reindexed from 1)		D225 D229
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y126 K173 D206 D230 D234
Catalytic site (residue number reindexed from 1) Y121 K168 D201 D225 D229
Enzyme Commision number 1.1.1.41: isocitrate dehydrogenase (NAD(+)).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004449 isocitrate dehydrogenase (NAD+) 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:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0045242 isocitrate dehydrogenase complex (NAD+)

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yvt, PDBe:5yvt, PDBj:5yvt
PDBsum5yvt
PubMed29453450
UniProtP50213|IDH3A_HUMAN Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Gene Name=IDH3A)

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