SMTL ID : 3ps3.1

Crystal structure of the Escherichia Coli LPXC/LPC-053 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: E.78, H.79, T.191, H.238, D.242, H.265 Ligands: L53.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.238, A:D.242, A:D.242

1 x L53: 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3S)-3-hydroxy-1-nitroso-1-oxobutan-2-yl]benzamide(Non-covalent)

L53.2: 24 residues within 4Å: Chain A: L.18, M.61, L.62, C.63, E.78, H.79, T.191, F.192, G.193, M.195, I.198, Q.202, C.207, G.210, S.211, F.212, A.215, V.217, H.238, D.242, H.265 Ligands: ZN.1, DMS.4, SO4.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.18, A:L.62, A:T.191, A:F.192, A:I.198, A:A.215, A:V.217 Hydrogen bonds: A:C.63, A:T.191, A:T.191 Water bridges: A:F.212 pi-Stacking: A:F.212

1 x UKW: 4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide(Non-covalent)

UKW.3: 5 residues within 4Å: Chain A: M.61, F.194, D.197, Y.200, L.201 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.200, A:Y.200, A:L.201 Hydrogen bonds: A:D.197

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 8 residues within 4Å: Chain A: M.61, L.62, G.193, F.194, D.197, I.198, L.201 Ligands: L53.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.197 DMS.5: 6 residues within 4Å: Chain A: H.163, I.166, F.192, G.193, F.194, V.218 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.161

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 1 residues within 4Å: Chain A: K.22 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.22 SO4.7: 5 residues within 4Å: Chain A: C.250, H.252, L.276, W.282, Y.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.284 SO4.8: 4 residues within 4Å: Chain A: T.60, M.61, L.62, R.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.61 Water bridges: A:L.62 Salt bridges: A:R.73 SO4.9: 6 residues within 4Å: Chain A: D.59, K.239, G.264, H.265, A.266 Ligands: L53.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.265 Water bridges: A:D.59, A:K.239, A:K.239, A:K.239, A:K.239, A:A.266 Salt bridges: A:K.239, A:H.265 SO4.10: 2 residues within 4Å: Chain A: K.22, K.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.23 Salt bridges: A:K.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, X. et al., Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold. Bioorg.Med.Chem. (2011)

Release Date

2011-01-19

Peptides

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

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