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Structure of PDB 1gpd Chain R Binding Site BS02

Receptor Information

>1gpd Chain R (length=333) Species: 6706 (Homarus americanus)

SKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHG
VFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTT
IEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTT
NCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQ
NIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECS
YDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLS
KTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA

Ligand information

• Ligand ID: NAD
• InChI: InChI=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
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=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 1.5.0: c1cc(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 3.341: NC(=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 1.5.0: c1cc(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
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 1gpd Chain R Residue 339

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1gpd Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): F8 R10 D32 T96 F99 S119 A120 C149 Y317
• Binding residue (residue number reindexed from 1): F8 R10 D31 T95 F98 S118 A119 C148 Y316
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 1.2.1.12: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating).

Gene Ontology

Molecular Function

• GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
• GO:0016491 oxidoreductase activity
• 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
• GO:0006096 glycolytic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1gpd, PDBe:1gpd, PDBj:1gpd
• PDBsum: 1gpd
• PubMed: 127793
• UniProt: P00357|G3P_HOMAM Glyceraldehyde-3-phosphate dehydrogenase

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