5MMO

E. coli DNA Gyrase B 24 kDa ATPase domain in complex with [3-(3-ethyl-ureido)-5-(pyridin-4-yl)-isoquinolin-8-yl-methyl]-carbamic acid prop-2-ynyl ester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/acs.jmedchem.6b01834
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A
234Escherichia coli O157:H7Mutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P0AES7 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AES7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
9JG
Query on 9JG

Download SDF File 
Download CCD File 
A
prop-2-ynyl ~{N}-[[3-(ethylcarbamoylamino)-5-pyridin-4-yl-isoquinolin-8-yl]methyl]carbamate
C22 H21 N5 O3
BRRCVBAIWLLLPK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.040α = 90.00
b = 72.040β = 90.00
c = 79.330γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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