Structure of PDB 6kdy Chain G Binding Site BS01

Receptor Information
>6kdy Chain G (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWM
IPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVS
IEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRI
AEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNE
MYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIG
ANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEA
ACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKD
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain6kdy Chain G Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6kdy Molecular basis for the function of the alpha beta heterodimer of human NAD-dependent isocitrate dehydrogenase.
Resolution3.02 Å
Binding residue
(original residue number in PDB)		I15 P71 L72 T74 N84 H263 G264 T265 A266 D268 I269 N276
Binding residue
(residue number reindexed from 1)		I13 P69 L70 T72 N82 H261 G262 T263 A264 D266 I267 N274
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y126 K173 D206 D230
Catalytic site (residue number reindexed from 1) Y124 K171 D204 D228
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
View graph for
Cellular Component
External links
PDB RCSB:6kdy, PDBe:6kdy, PDBj:6kdy
PDBsum6kdy
PubMed31515270
UniProtP50213|IDH3A_HUMAN Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Gene Name=IDH3A)

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