SMTL ID : 4ucv.1

Fragment bound to H.influenza NAD dependent DNA ligase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x IWH: 1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide(Non-covalent)

IWH.1: 8 residues within 4Å: Chain A: Y.18, Y.22, H.23, P.28, V.30, P.31, D.32, Y.35 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.22, A:D.32, A:Y.35, A:Y.35 Hydrogen bonds: A:V.30 Water bridges: A:V.30 pi-Stacking: A:Y.22, A:Y.35 IWH.3: 8 residues within 4Å: Chain B: Y.18, Y.22, H.23, P.28, V.30, P.31, D.32, Y.35 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.22, B:D.32, B:Y.35, B:Y.35 Hydrogen bonds: B:V.30, B:D.32 Water bridges: B:V.30 pi-Stacking: B:Y.22, B:Y.35

2 x I6G: 8-methoxy-2,3-dimethylquinoxalin-5-ol(Non-covalent)

I6G.2: 9 residues within 4Å: Chain A: L.80, S.81, L.82, E.114, E.174, Y.226, V.289, K.291 Chain B: W.310 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.82, A:Y.226, A:V.289, B:W.310 Hydrogen bonds: A:E.114, A:K.291 pi-Stacking: A:Y.226 I6G.4: 9 residues within 4Å: Chain A: W.310 Chain B: L.80, S.81, L.82, E.114, E.174, Y.226, V.289, K.291 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.82, B:Y.226, B:V.289, A:W.310 Hydrogen bonds: B:E.114, B:K.291 pi-Stacking: B:Y.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hale, M. et al., From Fragments to Leads: Novel Bacterial Nad+-Dependent DNA Ligase Inhibitors. Tetrahedron Lett. (2015)

Release Date

2015-10-14

Peptides

DNA LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA LIGASE

Related Entries With Identical Sequence