Structure of PDB 1wpq Chain B Binding Site BS02

Receptor Information
>1wpq Chain B (length=348) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASKKVCIVGSGNWGSAIAKIVGGNAAQLAQFDPRVTMWVFEEDIGGKKLT
EIINTQHENVKYLPGHKLPPNVVAVPDVVQAAEDADILIFVVPHQFIGKI
CDQLKGHLKANPTGISLIKGVDEGPNGLKLISEVIGERLGIPMSVLMGAN
IASEVADEKFCETTIGCKDPAQGQLLKELMQTPNFRITVVQEVDTVEICG
ALKNVVAVGAGFCDGLGFGDNTKAAVIRLGLMEMIAFAKLFCSGPVSSAT
FLESCGVADLITTCYGGRNRKVAEAFARTGKSIEQLEKELLNGQKLQGPE
TARELYSILQHKGLVDKFPLFMAVYKVCYEGQPVGEFIHCLQNHPEHM
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 chain1wpq Chain B Residue 3002 [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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PDB1wpq Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1)
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G12 N13 W14 F41 Y63 V92 V93 P94 F97 I119 K120 I152 A153 R269 Q295 K296 Q298
Binding residue
(residue number reindexed from 1)		G11 N12 W13 F40 Y62 V91 V92 P93 F96 I118 K119 I151 A152 R268 Q294 K295 Q297
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K204 T264
Catalytic site (residue number reindexed from 1) K203 T263
Enzyme Commision number 1.1.1.8: glycerol-3-phosphate dehydrogenase (NAD(+)).
Gene Ontology
Molecular Function
GO:0004368 glycerol-3-phosphate dehydrogenase (quinone) 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:0042803 protein homodimerization activity
GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
GO:0051287 NAD binding
GO:0141152 glycerol-3-phosphate dehydrogenase (NAD+) activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006072 glycerol-3-phosphate metabolic process
GO:0006094 gluconeogenesis
GO:0006116 NADH oxidation
GO:0006127 glycerophosphate shuttle
GO:0006734 NADH metabolic process
GO:0045821 positive regulation of glycolytic process
GO:0046168 glycerol-3-phosphate catabolic process
GO:0046486 glycerolipid metabolic process
GO:0071320 cellular response to cAMP
GO:0071356 cellular response to tumor necrosis factor
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1wpq, PDBe:1wpq, PDBj:1wpq
PDBsum1wpq
PubMed16460752
UniProtP21695|GPDA_HUMAN Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic (Gene Name=GPD1)

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