Structure of PDB 3exm Chain A Binding Site BS03

Receptor Information

>3exm Chain A (length=210) Species: 100226 (Streptomyces coelicolor A3(2))

GHWAPGSHILWRYRENGGPHVHIARPVTVVRDDADLLAVWLAPGTECVKP
VLADGTPVHLEPLATRYTKPRTVQRDQWFGTGVLKLARPGEAWSVWLFWD
PGWRFKNWYVNLERPLTRWEGGVDSEDHFLDISVHPDRTWHWRDEDEFAQ
ALRDGLMDPASAGRVRRAGRSAVAEIRAWGSPFADGWEHWRPDPAWPVPS
LPGDWDRTPA

Ligand information

• Ligand ID: GP2
• InChI: InChI=1S/C11H17N5O10P2/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(26-10)1-25-28(23,24)3-27(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
• InChIKey: OCJWYBKRHNXUME-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O)N=C(NC2=O)N
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(CP(=O)(O)O)O)O)O)N=C(NC2=O)N
• Formula: C11 H17 N5 O10 P2
• Name: PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER
• ChEMBL: CHEMBL1164951
• DrugBank: DB03486
• ZINC: ZINC000013549556
• PDB chain: 3exm Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3exm Structure and mechanism of a new family of prokaryotic nucleoside diphosphatases.
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): W100 F101 Y131 D149 D153
• Binding residue (residue number reindexed from 1): W78 F79 Y109 D127 D131
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 3.6.1.6: nucleoside diphosphate phosphatase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:3exm, PDBe:3exm, PDBj:3exm
• PDBsum: 3exm
• UniProt: Q9FBN7