SMTL ID : 4j1n.2 (1 other biounit)

Crystal structures of FabI from F. tularensis in complex with novel inhibitors based on the benzimidazole scaffold

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.33, L.34, L.35, S.39, I.40, V.60, C.82, D.83, V.84, S.110, I.111, A.112, F.113, I.138, L.164, T.165, Y.166, K.183, A.209, G.210, P.211, I.212, T.214, L.215, A.216, A.217, F.223 Ligands: 1JN.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.40, A:Y.166, A:Y.166, A:A.209 Hydrogen bonds: A:G.33, A:S.39, A:I.40, A:D.83, A:D.83, A:V.84, A:I.111, A:A.112, A:K.183, A:I.212, A:I.212, A:A.216 Water bridges: A:A.41, A:S.110, A:I.111 NAD.4: 26 residues within 4Å: Chain B: G.33, L.34, L.35, S.39, I.40, V.60, C.82, D.83, V.84, S.110, I.111, A.112, L.164, T.165, Y.166, K.183, A.209, G.210, P.211, I.212, T.214, L.215, A.216, A.217, F.223 Ligands: 1JN.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.40, B:Y.166, B:Y.166, B:A.209 Hydrogen bonds: B:G.33, B:I.40, B:D.83, B:V.84, B:I.111, B:A.112, B:K.183, B:I.212, B:I.212, B:T.214, B:A.216 Water bridges: B:L.215 NAD.6: 28 residues within 4Å: Chain C: G.33, L.34, L.35, S.39, I.40, V.60, C.82, D.83, V.84, S.110, I.111, A.112, F.113, I.138, L.164, T.165, Y.166, K.183, A.209, G.210, P.211, I.212, T.214, L.215, A.216, A.217, F.223 Ligands: 1JN.7 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.40, C:Y.166, C:Y.166, C:A.209 Hydrogen bonds: C:G.33, C:S.39, C:I.40, C:D.83, C:D.83, C:V.84, C:I.111, C:A.112, C:K.183, C:I.212, C:I.212, C:A.216 Water bridges: C:A.41, C:S.110, C:I.111 NAD.9: 26 residues within 4Å: Chain D: G.33, L.34, L.35, S.39, I.40, V.60, C.82, D.83, V.84, S.110, I.111, A.112, L.164, T.165, Y.166, K.183, A.209, G.210, P.211, I.212, T.214, L.215, A.216, A.217, F.223 Ligands: 1JN.10 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.40, D:Y.166, D:Y.166, D:A.209 Hydrogen bonds: D:G.33, D:I.40, D:D.83, D:V.84, D:I.111, D:A.112, D:K.183, D:I.212, D:I.212, D:T.214, D:A.216 Water bridges: D:L.215

4 x 1JN: 1-(4-methoxy-3-methylbenzyl)-1,5,6,7-tetrahydroindeno[5,6-d]imidazole(Non-covalent)

1JN.2: 13 residues within 4Å: Chain A: A.112, L.119, Y.166, M.173, P.174, S.175, Y.176, M.179, A.216, I.220, F.223, M.226 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.112, A:L.119, A:Y.166, A:Y.176, A:I.220, A:I.220, A:F.223 Hydrogen bonds: A:Y.176 pi-Stacking: A:Y.176, A:Y.176 1JN.5: 13 residues within 4Å: Chain B: A.112, F.113, L.119, Y.166, M.173, Y.176, M.179, A.216, I.220, F.223, M.226 Chain D: M.276 Ligands: NAD.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.112, B:L.119, B:Y.166, B:Y.176, B:A.216, B:I.220, B:I.220 pi-Stacking: B:Y.176, B:Y.176, B:F.223 1JN.7: 13 residues within 4Å: Chain C: A.112, L.119, Y.166, M.173, P.174, S.175, Y.176, M.179, A.216, I.220, F.223, M.226 Ligands: NAD.6 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:A.112, C:L.119, C:Y.166, C:Y.176, C:I.220, C:I.220, C:F.223 Hydrogen bonds: C:Y.176 pi-Stacking: C:Y.176, C:Y.176 1JN.10: 13 residues within 4Å: Chain B: M.276 Chain D: A.112, F.113, L.119, Y.166, M.173, Y.176, M.179, A.216, I.220, F.223, M.226 Ligands: NAD.9 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.112, D:L.119, D:Y.166, D:Y.176, D:A.216, D:I.220, D:I.220 pi-Stacking: D:Y.176, D:Y.176, D:F.223

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: E.170, A.184, E.187, A.188, R.191 Chain D: A.184 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.184, A:E.187, A:A.188, A:R.191, A:R.191 GOL.8: 6 residues within 4Å: Chain B: A.184 Chain C: E.170, A.184, E.187, A.188, R.191 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.184, C:E.187, C:A.188, C:R.191, C:R.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mehboob, S. et al., Structural and biological evaluation of a novel series of benzimidazole inhibitors of Francisella tularensis enoyl-ACP reductase (FabI). Bioorg.Med.Chem.Lett. (2015)

Release Date

2014-07-23

Peptides

Enoyl-[acyl-carrier-protein] reductase [NADH]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Enoyl-[acyl-carrier-protein] reductase [NADH]

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