Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.57 kDa 
• Atom Count: 2987 
• Modelled Residue Count: 322 
• Deposited Residue Count: 323 
• Unique protein chains: 1

4LH6

Crystal structure of a LigA inhibitor

• PDB DOI: 10.2210/pdb4LH6/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-30 Released: 2013-12-25 
• Deposition Author(s): Benenato, K., Wang, H., Mcguire, H.M., Davis, H., Gao, N., Prince, D.B., Jahic, H., Stokes, S.S., Boriack-Sjodin, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

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

• PubMed: 24287382 
• DOI: 10.1016/j.bmcl.2013.11.007
• Primary Citation of Related Structures:  
  4LH6, 4LH7


• 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 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.

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Organizational Affiliation: 

Department of Bioscience, Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Dr., Waltham, MA 02451, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	323	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: ligA, EF_0722 EC: 6.5.1.2
UniProt
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837V6  Go to UniProtKB:  Q837V6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN	C [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O
1X7	B [auth A]	4-amino-2-bromothieno[3,2-c]pyridine-7-carboxamide C8 H6 Br N3 O S KBJKAURPHBWEOT-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1X7	PDBBind:  4LH6	IC50: 7.70e+4 (nM) from 1 assay(s)
	Binding MOAD:  4LH6	IC50: 7.70e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.955	α = 90
b = 104.377	β = 90
c = 136.709	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-30 
• Released Date: 2013-12-25 
Deposition Author(s): Benenato, K., Wang, H., Mcguire, H.M., Davis, H., Gao, N., Prince, D.B., Jahic, H., Stokes, S.S., Boriack-Sjodin, P.A.

Revision History  

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