4GLX

DNA ligase A in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 

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:  4GLW

  • 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: 4
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A
586Escherichia coli (strain K12)Gene Names: ligA (dnaL, lig, lop, pdeC)
EC: 6.5.1.2
Find proteins for P15042 (Escherichia coli (strain K12))
Go to UniProtKB:  P15042
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (26-MER)B26synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3')C13synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3')D13synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0XS
Query on 0XS

Download SDF File 
Download CCD File 
A
2-amino-6-bromo-7-(trifluoromethyl)-1,8-naphthyridine-3-carboxamide
C10 H6 Br F3 N4 O
CENBBVPSOFGGNG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0XSKd: 16 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.990α = 90.00
b = 100.140β = 105.50
c = 86.570γ = 90.00
Software Package:
Software NamePurpose
INTEGRATEdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
RemDAqdata collection

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