4GLW

DNA ligase A in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2012.08.094
  • Primary Citation of Related Structures:  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 ...

    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.


    Organizational Affiliation

    Actelion Pharmaceuticals Ltd, Gewerbestrasse 16, CH-4123 Allschwil, Switzerland. jean-philippe.surivet@actelion.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A, B
305Streptococcus pneumoniae (strain P1031)Gene Names: ligA
EC: 6.5.1.2
Find proteins for C1CKI0 (Streptococcus pneumoniae (strain P1031))
Go to UniProtKB:  C1CKI0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0XT
Query on 0XT

Download SDF File 
Download CCD File 
A, B
7-methoxy-6-methylpteridine-2,4-diamine
C8 H10 N6 O
PBUUVJRZGWWXQU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NMN
Query on NMN

Download SDF File 
Download CCD File 
B
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
NICOTINAMIDE MONONUCLEOTIDE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0XTKd: 800 nM BINDINGMOAD
0XTKd: 800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 56.730α = 90.00
b = 56.730β = 90.00
c = 197.930γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
INTEGRATEdata reduction
RemDAqdata collection
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description