4HXZ

Pyrrolopyrimidine inhibitors of dna gyrase b and topoisomerase iv, part i: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.

Tari, L.W., Trzoss, M., Bensen, D.C., Li, X., Chen, Z., Lam, T., Zhang, J., Creighton, C.J., Cunningham, M.L., Kwan, B., Stidham, M., Shaw, K.J., Lightstone, F.C., Wong, S.E., Nguyen, T.B., Nix, J., Finn, J.

(2013) Bioorg Med Chem Lett 23: 1529-1536

  • DOI: https://doi.org/10.1016/j.bmcl.2012.11.032
  • Primary Citation of Related Structures:  
    4GEE, 4GFN, 4GGL, 4HXW, 4HXZ, 4HY1, 4HYM, 4HYP, 4HZ0, 4HZ5

  • PubMed Abstract: 

    • The bacterial topoisomerases DNA gyrase (GyrB) and topoisomerase IV (ParE) are essential enzymes that control the topological state of DNA during replication. The high degree of conservation in the ATP-binding pockets of these enzymes make them appealing targets for broad-spectrum inhibitor development ...

    The bacterial topoisomerases DNA gyrase (GyrB) and topoisomerase IV (ParE) are essential enzymes that control the topological state of DNA during replication. The high degree of conservation in the ATP-binding pockets of these enzymes make them appealing targets for broad-spectrum inhibitor development. A pyrrolopyrimidine scaffold was identified from a pharmacophore-based fragment screen with optimization potential. Structural characterization of inhibitor complexes conducted using selected GyrB/ParE orthologs aided in the identification of important steric, dynamic and compositional differences in the ATP-binding pockets of the targets, enabling the design of highly potent pyrrolopyrimidine inhibitors with broad enzymatic spectrum and dual targeting activity.

    Organizational Affiliation: 

    Trius Therapeutics, 6310 Nancy Ridge Dr., San Diego, CA 92121, USA. ltari@triusrx.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Topoisomerase IV, subunit BA, B390Francisella tularensis subsp. holarctica LVSMutation(s): 0 
Gene Names: DNA topoisomerase IV subunit B ParE, FTL_1726, parE
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for A0A0J9WZF0 (Francisella tularensis subsp. holarctica (strain LVS))
Explore A0A0J9WZF0 
Go to UniProtKB:  A0A0J9WZF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9WZF0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
19Y
Query on 19Y
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		6-ethyl-4-methoxy-2-(pyridin-3-ylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbaldehyde
C15 H14 N4 O2 S
LEMXQPJEGCAOFY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
19Y PDBBind:  4HXZ Ki: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.117α = 90
b = 162.874β = 92.71
c = 77.407γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary