Crystal Structure of E. coli GyraseB 24kDa in complex with 6-[(ethylcarbamoyl)amino]-4-[(4-methoxyphenyl)amino]-N-(pyridin-3-yl)pyridine-3-carboxamide

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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This is version 1.3 of the entry. See complete history


New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase.

Narramore, S.Stevenson, C.E.M.Maxwell, A.Lawson, D.M.Fishwick, C.W.G.

(2019) Bioorg Med Chem 27: 3546-3550

  • DOI: https://doi.org/10.1016/j.bmc.2019.06.015
  • Primary Citation of Related Structures:  
    6F86, 6F8J, 6F94, 6F96

  • PubMed Abstract: 

    Previously we have reported on a series of pyridine-3-carboxamide inhibitors of DNA gyrase and DNA topoisomerase IV that were designed using a computational de novo design approach and which showed promising antibacterial properties. Herein we describe the synthesis of additional examples from this series aimed specifically at DNA gyrase, along with crystal structures confirming the predicted mode of binding and in vitro ADME data which describe the drug-likeness of these compounds.

  • Organizational Affiliation

    School of Chemistry and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B221Escherichia coli O157:H7Mutation(s): 0 
Gene Names: gyrBZ5190ECs4634
Find proteins for P0AES6 (Escherichia coli (strain K12))
Explore P0AES6 
Go to UniProtKB:  P0AES6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AES6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on D0K

Download Ideal Coordinates CCD File 
B [auth A]6-(ethylcarbamoylamino)-4-[(4-methoxyphenyl)amino]-~{N}-pyridin-3-yl-pyridine-3-carboxamide
C21 H22 N6 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
D0K Binding MOAD:  6F96 IC50: 19 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.2α = 90
b = 100.2β = 90
c = 50.27γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description