Structure of PDB 5vn2 Chain D Binding Site BS01

Receptor Information

>5vn2 Chain D (length=253) Species: 224914 (Brucella melitensis bv. 1 str. 16M)

SRQRPVALVTGGRRGIGLGIARALAAKGFDLAITDRESDEAVIHELRGLG
GKVAFFKSDLAAVKTHEATVFAVLDAFGGIDCLVNNAGMGAVERGDFLAL
KPENFDTIMDVNLRGTVFFTQAVVKAMLAADEVRFPRSIVTISSVSSVMT
SPERLDYCISKAGLTAFVQGLALRLAEARIGVFEVRPGIIRTDMTAKVAA
RYDALIEGGLVPMKRWGEASDVGAIVAGLAGGDFIFATGSAIHADGGLSI
AKL

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: 5vn2 Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vn2 Crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis in complex with NAD
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G12 R14 R15 G16 I17 D36 R37 S59 D60 L61 N87 G89 S145 K162 P188 G189 I191 T193 M195 T196
• Binding residue (residue number reindexed from 1): G11 R13 R14 G15 I16 D35 R36 S58 D59 L60 N86 G88 S144 K161 P187 G188 I190 T192 M194 T195
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): S145 Y158 K162
• Catalytic site (residue number reindexed from 1): S144 Y157 K161
• Enzyme Commision number: 1.1.1.100: 3-oxoacyl-[acyl-carrier-protein] reductase.

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity

External links

• PDB: RCSB:5vn2, PDBe:5vn2, PDBj:5vn2
• PDBsum: 5vn2
• UniProt: Q8YJQ6