Structure of PDB 2dvm Chain D Binding Site BS01

Receptor Information

>2dvm Chain D (length=436) Species: 53953 (Pyrococcus horikoshii)

IREKALEFHKNNFPGNGKIEVIPKVSLESREELTLAYTPGVAEPCKEIAR
DPGKVYEYTSKGNLVAVVSDGSRILGLGNIGPLAGLPVMEGKALLFKRFG
GVDAFPIMIKEQEPNKFIDIVKAIAPTFGGINLEDIASPKCFYILERLRE
ELDIPVFHDDQQGTAAVVLAGLLNALKVVGKKISEITLALFGAGAAGFAT
LRILTEAGVKPENVRVVELVNGKPRILTSDLDLEKLFPYRGWLLKKTNGE
NIEGGPQEALKDADVLISFTRPGPGVIKPQWIEKMNEDAIVFPLANPVPE
ILPEEAKKAGARIVATGRSDYPNQINNLLGFPGIFRGALDVRARTITDSM
IIAAAKAIASIVEEPSEENIIPSPLNPIVYAREARAVAEEAMKEGVARTK
VKGEWVEEHTIRLIEFYENVIAPINKKRREYSKAIT

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: 2dvm Chain D Residue 2504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dvm NAD complex structure of PH1275 protein from Pyrococcus horikoshii
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): R74 T165 G195 A196 A197 V218 E219 L220 P225 F270 T271 L295 N297
• Binding residue (residue number reindexed from 1): R73 T164 G194 A195 A196 V217 E218 L219 P224 F269 T270 L294 N296
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y38 R74 K93 E135 D136 D160 D161 N297
• Catalytic site (residue number reindexed from 1): Y37 R73 K92 E134 D135 D159 D160 N296
• Enzyme Commision number: 1.1.1.38: malate dehydrogenase (oxaloacetate-decarboxylating).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003824 catalytic activity
• GO:0004470 malic enzyme 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

External links

• PDB: RCSB:2dvm, PDBe:2dvm, PDBj:2dvm
• PDBsum: 2dvm
• UniProt: O59029