Structure of PDB 3vdr Chain B Binding Site BS01

Receptor Information

>3vdr Chain B (length=260) Species: 511 (Alcaligenes faecalis)

MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLE
SKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIE
EFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASV
NKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAI
SQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTT
LSLDGGWTAR

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: 3vdr Chain B Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vdr Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): G11 T13 S14 I16 F36 D63 L64 N90 A91 G92 L113 S142 Y155 K159 G186 W187 V188 T190 L192 V193
• Binding residue (residue number reindexed from 1): G11 T13 S14 I16 F36 D63 L64 N90 A91 G92 L113 S142 Y155 K159 G186 W187 V188 T190 L192 V193
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): G15 N114 S142 Y155 K159 I200
• Catalytic site (residue number reindexed from 1): G15 N114 S142 Y155 K159 I200
• Enzyme Commision number: 1.1.1.30: 3-hydroxybutyrate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003858 3-hydroxybutyrate dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:3vdr, PDBe:3vdr, PDBj:3vdr
• PDBsum: 3vdr
• PubMed: 19342772
• UniProt: D0VWQ0