Crystal structure of a topoisomerase ATP inhibitor

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Discovery of a novel azaindole class of antibacterial agents targeting the ATPase domains of DNA gyrase and Topoisomerase IV.

Manchester, J.I.Dussault, D.D.Rose, J.A.Boriack-Sjodin, P.A.Uria-Nickelsen, M.Ioannidis, G.Bist, S.Fleming, P.Hull, K.G.

(2012) Bioorg Med Chem Lett 22: 5150-5156

  • DOI: https://doi.org/10.1016/j.bmcl.2012.05.128
  • Primary Citation of Related Structures:  
    4EM7, 4EMV

  • PubMed Abstract: 

    We present the discovery and optimization of a novel series of bacterial topoisomerase inhibitors. Starting from a virtual screening hit, activity was optimized through a combination of structure-based design and physical property optimization. Synthesis of fewer than a dozen compounds was required to achieve inhibition of the growth of methicillin-resistant Staphyloccus aureus (MRSA) at compound concentrations of 1.56 μM. These compounds simultaneously inhibit DNA gyrase and Topoisomerase IV at similar nanomolar concentrations, reducing the likelihood of the spontaneous occurrence of target-based mutations resulting in antibiotic resistance, an increasing threat in the treatment of serious infections.

  • Organizational Affiliation

    Infection Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, MA 02451, USA. john.manchester@astrazeneca.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase IV, B subunit226Streptococcus pneumoniae GA47373Mutation(s): 0 
Gene Names: ParESPAR94_0831
EC: 5.99.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0R9

Download Ideal Coordinates CCD File 
B [auth A]5-{2-(ethylcarbamoyl)-4-[3-(trifluoromethyl)-1H-pyrazol-1-yl]-1H-pyrrolo[2,3-b]pyridin-5-yl}pyridine-3-carboxylic acid
C20 H15 F3 N6 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
0R9 PDBBind:  4EMV IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.297α = 90
b = 94.92β = 90
c = 61.247γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata 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: 2012-08-01
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations