SMTL ID : 4fs3.1

Crystal structure of Staphylococcus aureus enoyl-ACP reductase in complex with NADP and AFN-1252

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x 0WD: [[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

0WD.1: 29 residues within 4Å: Chain A: G.13, I.14, A.15, S.19, I.20, T.38, Y.39, R.40, I.65, D.66, V.67, Q.68, S.93, I.94, A.95, I.120, T.145, T.146, Y.147, K.164, A.190, G.191, P.192, I.193, T.195, L.196, S.197, F.204 Ligands: 0WE.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.20, A:Y.147, A:A.190 Hydrogen bonds: A:G.13, A:A.15, A:I.20, A:R.40, A:D.66, A:V.67, A:I.94, A:Y.157, A:K.164, A:I.193, A:I.193, A:T.195, A:S.197 Water bridges: A:I.14, A:S.44, A:S.44, A:S.93, A:I.94, A:A.95, A:L.196 0WD.3: 29 residues within 4Å: Chain B: G.13, I.14, A.15, S.19, I.20, T.38, Y.39, R.40, I.65, D.66, V.67, Q.68, S.93, I.94, A.95, I.120, T.145, T.146, Y.147, K.164, A.190, G.191, P.192, I.193, T.195, L.196, S.197, F.204 Ligands: 0WE.4 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.20, B:Y.147, B:A.190 Hydrogen bonds: B:G.13, B:A.15, B:I.20, B:R.40, B:D.66, B:D.66, B:V.67, B:I.94, B:Y.157, B:Y.157, B:K.164, B:I.193, B:I.193, B:S.197 Water bridges: B:I.14, B:S.44, B:S.44, B:S.93, B:A.95, B:T.145, B:L.196 0WD.5: 29 residues within 4Å: Chain C: G.13, I.14, A.15, S.19, I.20, T.38, Y.39, R.40, I.65, D.66, V.67, Q.68, S.93, I.94, A.95, I.120, T.145, T.146, Y.147, K.164, A.190, G.191, P.192, I.193, T.195, L.196, S.197, F.204 Ligands: 0WE.6 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.20, C:Y.147, C:A.190 Hydrogen bonds: C:G.13, C:A.15, C:I.20, C:R.40, C:D.66, C:V.67, C:I.94, C:Y.157, C:K.164, C:I.193, C:I.193, C:T.195, C:S.197 Water bridges: C:I.14, C:S.44, C:S.44, C:S.93, C:I.94, C:A.95, C:L.196 0WD.7: 29 residues within 4Å: Chain D: G.13, I.14, A.15, S.19, I.20, T.38, Y.39, R.40, I.65, D.66, V.67, Q.68, S.93, I.94, A.95, I.120, T.145, T.146, Y.147, K.164, A.190, G.191, P.192, I.193, T.195, L.196, S.197, F.204 Ligands: 0WE.8 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:I.20, D:Y.147, D:A.190 Hydrogen bonds: D:G.13, D:A.15, D:I.20, D:R.40, D:D.66, D:D.66, D:V.67, D:I.94, D:Y.157, D:Y.157, D:K.164, D:I.193, D:I.193, D:S.197 Water bridges: D:I.14, D:S.44, D:S.44, D:S.93, D:A.95, D:T.145, D:L.196

4 x 0WE: N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)propanamide(Non-covalent)

0WE.2: 15 residues within 4Å: Chain A: F.96, A.97, M.99, L.102, Y.147, Q.155, N.156, Y.157, M.160, S.197, K.199, V.201, F.204, I.207 Ligands: 0WD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.102, A:Y.147, A:N.156, A:V.201, A:V.201, A:F.204, A:I.207 Hydrogen bonds: A:A.97, A:A.97 Water bridges: A:M.99 pi-Stacking: A:Y.157, A:Y.157 0WE.4: 15 residues within 4Å: Chain B: F.96, A.97, M.99, L.102, Y.147, Q.155, N.156, Y.157, M.160, S.197, K.199, V.201, F.204, I.207 Ligands: 0WD.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.102, B:Y.147, B:N.156, B:V.201, B:V.201, B:F.204, B:I.207 Hydrogen bonds: B:A.97, B:A.97, B:Y.157 Water bridges: B:M.99 pi-Stacking: B:Y.157, B:Y.157 0WE.6: 15 residues within 4Å: Chain C: F.96, A.97, M.99, L.102, Y.147, Q.155, N.156, Y.157, M.160, S.197, K.199, V.201, F.204, I.207 Ligands: 0WD.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.102, C:Y.147, C:N.156, C:V.201, C:V.201, C:F.204, C:I.207 Hydrogen bonds: C:A.97, C:A.97 Water bridges: C:M.99 pi-Stacking: C:Y.157, C:Y.157 0WE.8: 15 residues within 4Å: Chain D: F.96, A.97, M.99, L.102, Y.147, Q.155, N.156, Y.157, M.160, S.197, K.199, V.201, F.204, I.207 Ligands: 0WD.7 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.102, D:Y.147, D:N.156, D:V.201, D:V.201, D:F.204, D:I.207 Hydrogen bonds: D:A.97, D:A.97, D:Y.157 Water bridges: D:M.99 pi-Stacking: D:Y.157, D:Y.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaplan, N. et al., Mode of Action, In Vitro Activity, and In Vivo Efficacy of AFN-1252, a Selective Antistaphylococcal FabI Inhibitor. Antimicrob.Agents Chemother. (2012)

Release Date

2012-09-19

Peptides

Enoyl-[acyl-carrier-protein] reductase [NADPH] FabI: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Enoyl-[acyl-carrier-protein] reductase [NADPH] FabI