E. coli DNA Gyrase B 24 kDa ATPase domain in complex with 1-ethyl-3-[8-methyl-5-(2-methyl-pyridin-4-yl)-isoquinolin-3-yl]-urea

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Discovery and Optimization of Isoquinoline Ethyl Ureas as Antibacterial Agents.

Panchaud, P.Bruyere, T.Blumstein, A.C.Bur, D.Chambovey, A.Ertel, E.A.Gude, M.Hubschwerlen, C.Jacob, L.Kimmerlin, T.Pfeifer, T.Prade, L.Seiler, P.Ritz, D.Rueedi, G.

(2017) J Med Chem 60: 3755-3775

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01834
  • Primary Citation of Related Structures:  
    5MMN, 5MMO, 5MMP

  • PubMed Abstract: 

    Our strategy to combat resistant bacteria consisted of targeting the GyrB/ParE ATP-binding sites located on bacterial DNA gyrase and topoisomerase IV and not utilized by marketed antibiotics. Screening around the minimal ethyl urea binding motif led to the identification of isoquinoline ethyl urea 13 as a promising starting point for fragment evolution. The optimization was guided by structure-based design and focused on antibacterial activity in vitro and in vivo, culminating in the discovery of unprecedented substituents able to interact with conserved residues within the ATP-binding site. A detailed characterization of the lead compound highlighted the potential for treatment of the problematic fluoroquinolone-resistant MRSA, VRE, and S. pneumoniae, and the possibility to offer patients an intravenous-to-oral switch therapy was supported by the identification of a suitable prodrug concept. Eventually, hERG K-channel block was identified as the main limitation of this chemical series, and efforts toward its minimization are reported.

  • Organizational Affiliation

    Actelion Pharmaceuticals Ltd. , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B234Escherichia coli O157:H7Mutation(s): 0 
Gene Names: gyrBZ5190ECs4634
EC: (PDB Primary Data), (UniProt)
Find proteins for P0AES7 (Escherichia coli O157:H7)
Explore P0AES7 
Go to UniProtKB:  P0AES7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AES7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on O54

Download Ideal Coordinates CCD File 
B [auth A]1-ethyl-3-[8-methyl-5-(2-methylpyridin-4-yl)isoquinolin-3-yl]urea
C19 H20 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
O54 Binding MOAD:  5MMN IC50: 125 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.52α = 90
b = 71.52β = 90
c = 78.95γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references