4P8O

S. aureus gyrase bound to an aminobenzimidazole urea inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Second-generation antibacterial benzimidazole ureas: discovery of a preclinical candidate with reduced metabolic liability.

Grillot, A.L.Tiran, A.L.Shannon, D.Krueger, E.Liao, Y.O'Dowd, H.Tang, Q.Ronkin, S.Wang, T.Waal, N.Li, P.Lauffer, D.Sizensky, E.Tanoury, J.Perola, E.Grossman, T.H.Doyle, T.Hanzelka, B.Jones, S.Dixit, V.Ewing, N.Liao, S.Boucher, B.Jacobs, M.Bennani, Y.Charifson, P.S.

(2014) J.Med.Chem. 57: 8792-8816

  • DOI: 10.1021/jm500563g

  • PubMed Abstract: 
  • Compound 3 is a potent aminobenzimidazole urea with broad-spectrum Gram-positive antibacterial activity resulting from dual inhibition of bacterial gyrase (GyrB) and topoisomerase IV (ParE), and it demonstrates efficacy in rodent models of bacterial ...

    Compound 3 is a potent aminobenzimidazole urea with broad-spectrum Gram-positive antibacterial activity resulting from dual inhibition of bacterial gyrase (GyrB) and topoisomerase IV (ParE), and it demonstrates efficacy in rodent models of bacterial infection. Preclinical in vitro and in vivo studies showed that compound 3 covalently labels liver proteins, presumably via formation of a reactive metabolite, and hence presented a potential safety liability. The urea moiety in compound 3 was identified as being potentially responsible for reactive metabolite formation, but its replacement resulted in loss of antibacterial activity and/or oral exposure due to poor physicochemical parameters. To identify second-generation aminobenzimidazole ureas devoid of reactive metabolite formation potential, we implemented a metabolic shift strategy, which focused on shifting metabolism away from the urea moiety by introducing metabolic soft spots elsewhere in the molecule. Aminobenzimidazole urea 34, identified through this strategy, exhibits similar antibacterial activity as that of 3 and did not label liver proteins in vivo, indicating reduced/no potential for reactive metabolite formation.


    Organizational Affiliation

    Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A, B
187Staphylococcus aureus (strain MRSA252)Mutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for Q6GKU0 (Staphylococcus aureus (strain MRSA252))
Go to UniProtKB:  Q6GKU0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
883
Query on 883

Download SDF File 
Download CCD File 
A, B
1-ethyl-3-[5-(5-fluoropyridin-3-yl)-7-(pyrimidin-2-yl)-1H-benzimidazol-2-yl]urea
C19 H16 F N7 O
FKCGKEHVIVGGDU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.460α = 90.00
b = 55.730β = 100.42
c = 50.800γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-31 
  • Released Date: 2014-10-29 
  • Deposition Author(s): Jacobs, M.D.

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2015-09-30
    Type: Data collection