Crystal structure of E. coli Gyrase B co-complexed with PROP-2-YN-1-YL {[5-(4-PIPERIDIN-1-YL-2-PYRIDIN-3-YL-1,3-THIAZOL-5-YL)-1H-PYRAZOL-3-YL]METHYL}CARBAMATE inhibitor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery of pyrazolthiazoles as novel and potent inhibitors of bacterial gyrase.

Ronkin, S.M.Badia, M.Bellon, S.Grillot, A.L.Gross, C.H.Grossman, T.H.Mani, N.Parsons, J.D.Stamos, D.Trudeau, M.Wei, Y.Charifson, P.S.

(2010) Bioorg Med Chem Lett 20: 2828-2831

  • DOI: https://doi.org/10.1016/j.bmcl.2010.03.052
  • Primary Citation of Related Structures:  
    3G75, 3G7B, 3G7E

  • PubMed Abstract: 

    Bacterial DNA gyrase is an attractive target for the investigation of new antibacterial agents. Inhibitors of the GyrB subunit, which contains the ATP-binding site, are described in this communication. Novel, substituted 5-(1H-pyrazol-3-yl)thiazole compounds were identified as inhibitors of bacterial gyrase. Structure-guided optimization led to greater enzymatic potency and moderate antibacterial potency. Data are presented for the demonstration of selective enzyme inhibition of Escherichia coli GyrB over Staphylococcus aureus GyrB.

  • Organizational Affiliation

    Vertex Pharmaceuticals Inc., 130 Waverly Street, Cambridge, MA 02139, USA. steven_Ronkin@vrtx.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B203Escherichia coliMutation(s): 0 
Gene Names: ECs4634
Find proteins for C3SLN3 (Escherichia coli)
Explore C3SLN3 
Go to UniProtKB:  C3SLN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3SLN3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B46

Download Ideal Coordinates CCD File 
B [auth A]prop-2-yn-1-yl {[5-(4-piperidin-1-yl-2-pyridin-3-yl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methyl}carbamate
C21 H22 N6 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.4α = 90
b = 95.4β = 90
c = 51.25γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-07-03
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description