Structure of PDB 2vyv Chain D Binding Site BS02

Receptor Information
>2vyv Chain D (length=334) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKVGINGFGRIGRLVLRVCMEKGVRVVAVNDPFIDPEYMVYMFKYDSTH
GRYKGTVEHKNGRLVVDNLEINVFQCKEPKEIPWSSVGNPYVVEATGVYL
SIEAASGHISSGARRVIVTAPSPDAPMLVMGVNEKDYNPGSMTVVSNASC
TTNCLAPLAKVIHERFGIVEGLMTTVHAYTATQKTVDGPSKKDWRGGRGA
HQNIIPSSTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLAQP
ASYTAIKEAVKAAAKGPMAGILAYTEDQVVSTDFNGDSHSSIFDAKAGIA
LNDNFVKLVSWYDNEYGYSHRVVDLLRYMFSREK
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 chain2vyv Chain D Residue 1340 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vyv Structure of Insoluble Rat Sperm Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) Via Heterotetramer Formation with Escherichia Coli Gapdh Reveals Target for Contraceptive Design.
Resolution2.38 Å
Binding residue
(original residue number in PDB)		N6 G7 G9 R10 I11 D31 P32 F33 T95 G96 T118 A149 N313 Y317
Binding residue
(residue number reindexed from 1)		N7 G8 G10 R11 I12 D32 P33 F34 T96 G97 T119 A150 N314 Y318
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) C149 H176
Catalytic site (residue number reindexed from 1) C150 H177
Enzyme Commision number 1.2.1.12: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating).
Gene Ontology
Molecular Function
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006006 glucose metabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:2vyv, PDBe:2vyv, PDBj:2vyv
PDBsum2vyv
PubMed19542219
UniProtQ9ESV6|G3PT_RAT Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (Gene Name=Gapdhs)

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