4GEE

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: 1.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bmcl.2012.11.032
  • Primary Citation of Related Structures:  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 appea ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A
215Enterococcus faecalis (strain ATCC 700802 / V583)Gene Names: gyrB
EC: 5.99.1.3
Find proteins for Q839Z1 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q839Z1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
0WT
Query on 0WT

Download SDF File 
Download CCD File 
A
(1R,5S,6s)-3-[5-chloro-6-ethyl-2-(pyrimidin-5-yloxy)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-amine
C17 H18 Cl N7 O
YZRGALHCPBRTES-MSRIBSCDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0WTKi: <1 nM BINDINGMOAD
0WTKi: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.930α = 90.00
b = 58.080β = 90.00
c = 66.250γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references