4LH6

Crystal structure of a LigA inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Identification through structure-based methods of a bacterial NAD(+)-dependent DNA ligase inhibitor that avoids known resistance mutations.

Murphy-Benenato, K., Wang, H., McGuire, H.M., Davis, H.E., Gao, N., Prince, D.B., Jahic, H., Stokes, S.S., Boriack-Sjodin, P.A.

(2014) Bioorg.Med.Chem.Lett. 24: 360-366

  • DOI: 10.1016/j.bmcl.2013.11.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • In an attempt to identify novel inhibitors of NAD(+)-dependent DNA ligase (LigA) that are not affected by a known resistance mutation in the adenosine binding pocket, a detailed analysis of the binding sites of a variety of bacterial ligases was perf ...

    In an attempt to identify novel inhibitors of NAD(+)-dependent DNA ligase (LigA) that are not affected by a known resistance mutation in the adenosine binding pocket, a detailed analysis of the binding sites of a variety of bacterial ligases was performed. This analysis revealed several similarities to the adenine binding region of kinases, which enabled a virtual screen of known kinase inhibitors. From this screen, a thienopyridine scaffold was identified that was shown to inhibit bacterial ligase. Further characterization through structure and enzymology revealed the compound was not affected by a previously disclosed resistance mutation in Streptococcus pneumoniae LigA, Leu75Phe. A subsequent medicinal chemistry program identified substitutions that resulted in an inhibitor with moderate activity across various Gram-positive bacterial LigA enzymes.

    Organizational Affiliation: 

    Department of Chemistry, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Dr., Waltham, MA 02451, United States. Electronic address: kerry.benenato@astrazeneca.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A
323Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 0 
Gene Names: ligA
EC: 6.5.1.2
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q837V6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT
Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
1X7
Query on 1X7
Download SDF File 
Download CCD File 
A
4-amino-2-bromothieno[3,2-c]pyridine-7-carboxamide
C8 H6 Br N3 O S
KBJKAURPHBWEOT-UHFFFAOYSA-N
 Ligand Interaction
NMN
Query on NMN
Download SDF File 
Download CCD File 
A
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
NICOTINAMIDE MONONUCLEOTIDE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1X7IC50: 77000 nM BINDINGMOAD
1X7IC50: 77000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 48.955α = 90.00
b = 104.377β = 90.00
c = 136.709γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement
CrystalCleardata collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-08
    Type: Database references