4HY1

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: 1.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


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

  • 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
Topoisomerase IV, subunit B
A, B
390Francisella tularensis subsp. holarctica (strain LVS)Gene Names: parE
EC: 5.99.1.3
Find proteins for A0A0J9WZF0 (Francisella tularensis subsp. holarctica (strain LVS))
Go to UniProtKB:  A0A0J9WZF0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
19X
Query on 19X

Download SDF File 
Download CCD File 
A, B
6-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)-1H-isoindol-1-one
C20 H19 Cl N6 O S
MFHNBYVWNDLIQC-LLVKDONJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
19XKi: 2 nM BINDINGMOAD
19XKi: 2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.164α = 90.00
b = 130.282β = 98.12
c = 80.270γ = 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
  • Version 1.2: 2018-01-24
    Type: Structure summary