Structure of PDB 8grd Chain A Binding Site BS02

Receptor Information
>8grd Chain A (length=325) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGWMIPSEA
KESMDKNKMGLKGPLKTPPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTD
VNIVTIRENTEGEYSGIEHVIVDGVVASIKLITEGASKRIAEFAFEYARN
NHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYLDTVCLNM
VQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESV
HGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACFATIKDGK
SLTKDLGGNAKCSDFTEEICRRVKD
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8grd Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8grd Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction.
Resolution2.699 Å
Binding residue
(original residue number in PDB)		Y204 T207
Binding residue
(residue number reindexed from 1)		Y192 T195
Annotation score3
Enzymatic activity
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:8grd, PDBe:8grd, PDBj:8grd
PDBsum8grd
PubMed36375638
UniProtP50213|IDH3A_HUMAN Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Gene Name=IDH3A)

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