Crystal structure of a topoisomerase ATP inhibitor

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Fragment-to-Hit-to-Lead Discovery of a Novel Pyridylurea Scaffold of ATP Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents.

Basarab, G.S.Manchester, J.I.Bist, S.Boriack-Sjodin, P.A.Dangel, B.Illingworth, R.Sherer, B.A.Sriram, S.Uria-Nickelsen, M.Eakin, A.E.

(2013) J Med Chem 56: 8712-8735

  • DOI: https://doi.org/10.1021/jm401208b
  • Primary Citation of Related Structures:  
    4LP0, 4LPB

  • PubMed Abstract: 

    The discovery and optimization of a new class of bacterial topoisomerase (DNA gyrase and topoisomerase IV) inhibitors binding in the ATP domain are described. A fragment molecule, 1-ethyl-3-(2-pyridyl)urea, provided sufficiently potent enzyme inhibition (32 μM) to prompt further analogue work. Acids and acid isosteres were incorporated at the 5-pyridyl position of this fragment, bridging to a key asparagine residue, improving enzyme inhibition, and leading to measurable antibacterial activity. A CF3-thiazole substituent at the 4-pyridyl position improved inhibitory potency due to a favorable lipophilic interaction. Promising antibacterial activity was seen versus the Gram-positive pathogens Staphylococcus aureus and Streptococcus pneumoniae and the Gram-negative pathogens Haemophilus influenzae and Moraxella catarrhalis . Precursor metabolite incorporation and mutant analysis studies support the mode-of-action, blockage of DNA synthesis by dual target topoisomerase inhibition. Compound 35 was efficacious in a mouse S. aureus disease model, where a 4.5-log reduction in colony forming units versus control was demonstrated.

  • Organizational Affiliation

    Infection Innovative Medicines, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Topoisomerase IV subunit B226Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: parEspr0756
EC: 5.99.1
Find proteins for Q8DQB5 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DQB5 
Go to UniProtKB:  Q8DQB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DQB5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1YM

Download Ideal Coordinates CCD File 
B [auth A]6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid
C18 H14 F3 N5 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
1YM PDBBind:  4LP0 IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.875α = 90
b = 94.333β = 90
c = 62.27γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations