4GLW

DNA ligase A in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4GLW/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Streptococcus pneumoniae P1031
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-15 Released: 2012-10-10 
• Deposition Author(s): Prade, L., Lange, R., Tidten-Luksch, N., Chambovey, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity.

Surivet, J.P., Lange, R., Hubschwerlen, C., Keck, W., Specklin, J.L., Ritz, D., Bur, D., Locher, H., Seiler, P., Strasser, D.S., Prade, L., Kohl, C., Schmitt, C., Chapoux, G., Ilhan, E., Ekambaram, N., Athanasiou, A., Knezevic, A., Sabato, D., Chambovey, A., Gaertner, M., Enderlin, M., Boehme, M., Sippel, V., Wyss, P.

(2012) Bioorg Med Chem Lett 22: 6705-6711

• PubMed: 23006603 
• DOI: https://doi.org/10.1016/j.bmcl.2012.08.094
• Primary Citation of Related Structures:  
  4GLW, 4GLX


• PubMed Abstract: 
  

  A series of 2-amino-[1,8]-naphthyridine-3-carboxamides (ANCs) with potent inhibition of bacterial NAD(+)-dependent DNA ligases (LigAs) evolved from a 2,4-diaminopteridine derivative discovered by HTS. The design was guided by several highly resolved X-ray structures of our inhibitors in complex with either Streptococcus pneumoniae or Escherichia coli LigA. The structure-activity-relationship based on the ANC scaffold is discussed. The in-depth characterization of 2-amino-6-bromo-7-(trifluoromethyl)-[1,8]-naphthyridine-3-carboxamide, which displayed promising in vitro (MIC Staphylococcus aureus 1 mg/L) and in vivo anti-staphylococcal activity, is presented.

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Organizational Affiliation: 

Actelion Pharmaceuticals Ltd, Gewerbestrasse 16, CH-4123 Allschwil, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.13 kDa 
• Atom Count: 4,384 
• Modelled Residue Count: 556 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A, B	305	Streptococcus pneumoniae P1031	Mutation(s): 0  Gene Names: ligA, SPP_1122 EC: 6.5.1.2
UniProt
Find proteins for C1CKI0 (Streptococcus pneumoniae (strain P1031)) Explore C1CKI0  Go to UniProtKB:  C1CKI0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN	G [auth B]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O
0XT	D [auth A], F [auth B]	7-methoxy-6-methylpteridine-2,4-diamine C8 H10 N6 O PBUUVJRZGWWXQU-UHFFFAOYSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
0XT	PDBBind:  4GLW	Kd: 800 (nM) from 1 assay(s)
	Binding MOAD:  4GLW	Kd: 800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.73	α = 90
b = 56.73	β = 90
c = 197.93	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
RemDAq	data collection
INTEGRATE	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Prade, L., Lange, R., Tidten-Luksch, N., Chambovey, A.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations