4EM7

Crystal structure of a topoisomerase ATP inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2012.05.128
  • Primary Citation of Related Structures:  

  • 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. Synth ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase IV, B subunit
A
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0RA
Query on 0RA

Download SDF File 
Download CCD File 
A
3-[3-(1H-pyrrolo[2,3-b]pyridin-5-yl)phenyl]propanoic acid
C16 H14 N2 O2
HMZZTTNTVUPEKW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0RAIC50: 7700 nM BINDINGMOAD
0RAIC50: 7700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.866α = 90.00
b = 94.569β = 90.00
c = 60.871γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release