SMTL ID : 4uco.1

Fragment bound to H.influenza NAD dependent DNA ligase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x D41: 7-amino-2-tert-butyl-4-(1H-pyrrol-2-yl)pyrido[2,3-d]pyrimidine-6-carboxamide(Non-covalent)

D41.1: 15 residues within 4Å: Chain A: L.80, S.81, L.82, E.114, P.115, K.116, L.117, A.121, R.137, E.174, Y.226, V.289, K.291 Chain B: P.308, A.311 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.80, A:L.82, A:L.82, A:A.121, A:Y.226, A:V.289, B:P.308, B:A.311 Hydrogen bonds: A:E.114, A:E.114, A:L.117, A:L.117, A:K.291 pi-Stacking: A:Y.226, A:Y.226 D41.3: 15 residues within 4Å: Chain A: P.308, A.311 Chain B: L.80, S.81, L.82, E.114, P.115, K.116, L.117, A.121, R.137, E.174, Y.226, V.289, K.291 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.80, B:L.82, B:L.82, B:A.121, B:Y.226, B:V.289, A:P.308, A:A.311 Hydrogen bonds: B:E.114, B:L.117, B:L.117, B:K.291 pi-Stacking: B:Y.226, B:Y.226

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

IWH.2: 8 residues within 4Å: Chain A: Y.18, Y.22, H.23, P.28, V.30, P.31, D.32, Y.35 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.22, A:D.32, A:Y.35, A:Y.35 Hydrogen bonds: A:V.30 pi-Stacking: A:Y.22, A:Y.35 IWH.4: 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:Y.22 pi-Stacking: B:Y.22, B:Y.35

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

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