Structure of PDB 6kdy Chain B Binding Site BS01

Receptor Information
>6kdy Chain B (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFPVTMLPGDGVGPELMHAVKEVFKAAAVPVEFQEHHLSEVQNMASEEKL
EQVLSSMKENKVAIIGKIHTPMEYKGELASYDMRLRRKLDLFANVVHVKS
LPGYMTRHNNLDLVIIREQTEGEYSSLEHESARGVIECLKIVTRAKSQRI
AKFAFDYATKKGRGKVTAVHKANIMKLGDGLFLQCCEEVAELYPKIKFET
MIIDNCCMQLVQNPYQFDVLVMPNLYGNIIDNLAAGLVGGAGVVPGESYS
AEYAVFETGARHPFAQAVGRNIANPTAMLLSASNMLRHLNLEYHSSMIAD
AVKKVIKVGKVRTSDMGGYATCHDFTEEICRRVKDLDENLY
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 A 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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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)		N186 I215 N218
Binding residue
(residue number reindexed from 1)		N173 I202 N205
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y137 K184 D217 N241
Catalytic site (residue number reindexed from 1) Y124 K171 D204 N228
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
Biological Process
GO:0006099 tricarboxylic acid cycle

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6kdy, PDBe:6kdy, PDBj:6kdy
PDBsum6kdy
PubMed31515270
UniProtO43837|IDH3B_HUMAN Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial (Gene Name=IDH3B)

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