4CC5

Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fragment-Based Discovery of 6-Azaindazoles as Inhibitors of Bacterial DNA Ligase.

Howard, S.Amin, N.Benowitz, A.B.Chiarparin, E.Cui, H.Deng, X.Heightman, T.D.Holmes, D.J.Hopkins, A.Huang, J.Jin, Q.Kreatsoulas, C.Martin, A.C.L.Massey, F.Mccloskey, L.Mortenson, P.N.Pathuri, P.Tisi, D.Williams, P.A.

(2013) Acs Med.Chem.Lett. 4: 1208

  • DOI: 10.1021/ml4003277
  • Primary Citation of Related Structures:  
  • Also Cited By: 5FPR, 5FPO

  • PubMed Abstract: 
  • Herein we describe the application of fragment-based drug design to bacterial DNA ligase. X-ray crystallography was used to guide structure-based optimization of a fragment-screening hit to give novel, nanomolar, AMP-competitive inhibitors. The lead ...

    Herein we describe the application of fragment-based drug design to bacterial DNA ligase. X-ray crystallography was used to guide structure-based optimization of a fragment-screening hit to give novel, nanomolar, AMP-competitive inhibitors. The lead compound 13 showed antibacterial activity across a range of pathogens. Data to demonstrate mode of action was provided using a strain of S. aureus, engineered to overexpress DNA ligase.


    Organizational Affiliation

    Astex Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA LIGASE
A
318Staphylococcus aureusMutation(s): 0 
Gene Names: ligA (lig)
EC: 6.5.1.2
Find proteins for Q9AIU7 (Staphylococcus aureus)
Go to UniProtKB:  Q9AIU7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L5V
Query on L5V

Download SDF File 
Download CCD File 
A
2-chloranyl-6-(1H-1,2,4-triazol-3-yl)pyrazine
C6 H4 Cl N5
KOARCKONUFDYQJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L5VKd: 38000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 170.363α = 90.00
b = 39.523β = 90.13
c = 48.587γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release