Structure of PDB 3uf0 Chain A Binding Site BS01

Receptor Information

>3uf0 Chain A (length=249) Species: 471853 (Beutenbergia cavernae DSM 12333)

GPFSLAGRTAVVTGAGSGIGRAIAHGYARAGAHVLAWGRTDGVKEVADEI
ADGGGSAEAVVADLADLEGAANVAEELAATRRVDVLVNNAGIIARAPAEE
VSLGRWREVLTVNLDAAWVLSRSFGTAMLAHGSGRIVTIASMLSFQGGRN
VAAYAASKHAVVGLTRALASEWAGRGVGVNALAPGYVVTANTAALRADDE
RAAEITARIPAGRWATPEDMVGPAVFLASDAASYVHGQVLAVDGGWLAS

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: 3uf0 Chain A Residue 274

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3uf0 Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G16 S19 G20 I21 R41 D65 L66 N91 G93 I94 I141 A142 S143 Y156 K160 P186 G187 V189 T191 N193 T194
• Binding residue (residue number reindexed from 1): G14 S17 G18 I19 R39 D63 L64 N89 G91 I92 I139 A140 S141 Y154 K158 P184 G185 V187 T189 N191 T192
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): G20 S143 V153 Y156 K160
• Catalytic site (residue number reindexed from 1): G18 S141 V151 Y154 K158
• Enzyme Commision number: 1.1.1.125: 2-deoxy-D-gluconate 3-dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008678 2-deoxy-D-gluconate 3-dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

External links

• PDB: RCSB:3uf0, PDBe:3uf0, PDBj:3uf0
• PDBsum: 3uf0
• UniProt: C5BY10