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 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1021/ml4003277
  • Primary Citation of Related Structures:  
    4CC5, 4CC6

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA LIGASE318Staphylococcus aureusMutation(s): 0 
EC: 6.5.1.2
UniProt
Find proteins for Q9AIU7 (Staphylococcus aureus)
Explore Q9AIU7 
Go to UniProtKB:  Q9AIU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AIU7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L5V
Query on L5V

Download Ideal Coordinates CCD File 
C [auth A]2-chloranyl-6-(1H-1,2,4-triazol-3-yl)pyrazine
C6 H4 Cl N5
KOARCKONUFDYQJ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
L5V Binding MOAD:  4CC5 Kd: 3.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.363α = 90
b = 39.523β = 90.13
c = 48.587γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description