SMTL ID : 4lh6.1

Crystal structure of a LigA inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x 1X7: 4-amino-2-bromothieno[3,2-c]pyridine-7-carboxamide(Non-covalent)

1X7.1: 10 residues within 4Å: Chain A: Y.87, L.89, E.118, L.119, K.120, I.121, E.175, Y.227, V.289, K.291 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.289 Hydrogen bonds: A:E.118, A:K.120, A:I.121, A:I.121, A:K.291 Water bridges: A:L.119, A:E.175 Halogen bonds: A:Y.87

1 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.2: 12 residues within 4Å: Chain A: Y.25, S.26, Y.29, Y.30, P.35, V.37, E.38, D.39, Y.42, D.43, Y.46, R.158 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.29, A:Y.30, A:Y.42 Hydrogen bonds: A:D.39, A:D.39, A:Y.42, A:D.43 Water bridges: A:S.26, A:V.37, A:Y.42, A:Y.42 Salt bridges: A:R.158 pi-Stacking: A:Y.29, A:Y.42

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: W.268, I.271, H.275, Y.314 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.268, A:I.271 Hydrogen bonds: A:Y.314, A:Y.314 Salt bridges: A:H.275

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: A.218, R.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.220 NA.5: 2 residues within 4Å: Chain A: E.276, S.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.276 Water bridges: A:S.279, A:S.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murphy-Benenato, K. et al., Identification through structure-based methods of a bacterial NAD(+)-dependent DNA ligase inhibitor that avoids known resistance mutations. Bioorg.Med.Chem.Lett. (2014)

Release Date

2013-12-25

Peptides

DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase

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