4GLW

DNA ligase A in complex with inhibitor


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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, 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligaseA, B305Streptococcus pneumoniae P1031Mutation(s): 0 
Gene Names: ligASPP_1122
EC: 6.5.1.2
UniProt
Find proteins for C1CKI0 (Streptococcus pneumoniae (strain P1031))
Explore C1CKI0 
Go to UniProtKB:  C1CKI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1CKI0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NMN
Query on NMN

Download Ideal Coordinates CCD File 
G [auth B]BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
 Ligand Interaction
0XT
Query on 0XT

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
7-methoxy-6-methylpteridine-2,4-diamine
C8 H10 N6 O
PBUUVJRZGWWXQU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 56.73α = 90
b = 56.73β = 90
c = 197.93γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
RemDAqdata collection
INTEGRATEdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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