Structure of PDB 5va8 Chain D Binding Site BS01

Receptor Information

>5va8 Chain D (length=261) Species: 391038 (Paraburkholderia phymatum STM815)

HHMDLGIAGKSALVCAASKGLGRGCAEALAAEGVNVTIVARTPETLDATA
AAIRANAGVDVQAVACDITTPEGRAAALAACPQPDILVNNAGGPPPGDFR
NFTHDDWIRALEANMLTPIELIRATIDGMISRGFGRVVNITSSSVKAPID
VLGLSNGARSGLTGFIAGVARKVAPNGVTINNLLPGIFDTDRIAVTFDAA
AKAQNISVDEARKQRMATIPARRFGTPDEFGRACAFLCSVHAGYITGQNW
LIDGGAYPGTY

Ligand information

• Ligand ID: NAP
• InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: XJLXINKUBYWONI-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)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[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]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)OP(=O)(O)O)O)O)O)C(=O)N
• Formula: C21 H28 N7 O17 P3
• Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
  2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL295069
• DrugBank: DB03461
• PDB chain: 5va8 Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5va8 Crystal Structure of Short-chain dehydrogenase/reductase SDR from Burkholderia phymatum in complex with NADP
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): A14 S16 G18 L19 A38 R39 T40 D65 I66 N88 A89 G90 G91 R157 P183 G184 I185 F186 T188
• Binding residue (residue number reindexed from 1): A16 S18 G20 L21 A40 R41 T42 D67 I68 N90 A91 G92 G93 R159 P185 G186 I187 F188 T190
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): S140 R157
• Catalytic site (residue number reindexed from 1): S142 R159

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding

External links

• PDB: RCSB:5va8, PDBe:5va8, PDBj:5va8
• PDBsum: 5va8
• UniProt: B2JE32