ISDA

Deposition Date 2012-08-15

Release Date 2012-10-10

Last Version Date 2024-02-28

Entry Detail

PDB ID:

4GLX

Keywords:

LIGASE/LIGASE INHIBITOR/DNA

Title:

DNA ligase A in complex with inhibitor

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 83333)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.90 Å

R-Value Free:

0.24

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA ligase
Gene (Uniprot):ligA
Chain IDs:D (auth: A)
Chain Length:586
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P15042 Pfam ID:PF22745, PF01653, PF03120, PF03119, PF14520, PF00633 EC:6.5.1.2

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (26-MER)
Chain IDs:A (auth: B)
Chain Length:26
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3')
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3')
Chain IDs:C (auth: D)
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

0XS

SO4

Primary Citation

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.Show

Bioorg.Med.Chem.Lett. 22 6705 6711 (2012)

PMID: 23006603 DOI: 10.1016/j.bmcl.2012.08.094

Abstact

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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Primary Citation of related structures