SMTL ID : 7k9a.2 (1 other biounit)

Crystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x W8P: N-hydroxy-N-[(1R)-2-{5-[(4-{[2-(hydroxymethyl)-1H-imidazol-1-yl]methyl}phenyl)ethynyl]-1H-benzotriazol-1-yl}-1-(methylsulfanyl)ethyl]formamide(Non-covalent)

W8P.1: 14 residues within 4Å: Chain A: E.134, S.136, E.138, R.143, V.145, S.155, F.156, E.157, Q.171, A.172, R.258, G.259, F.260 Ligands: SO4.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.143, A:R.143, A:V.145, A:R.258, A:F.260 Hydrogen bonds: A:S.155, A:G.259, A:G.259

1 x W4P: N-hydroxy-N-[(1S)-2-{5-[(4-{[2-(hydroxymethyl)-1H-imidazol-1-yl]methyl}phenyl)ethynyl]-1H-benzotriazol-1-yl}-1-(methylsulfanyl)ethyl]formamide(Non-covalent)

W4P.2: 22 residues within 4Å: Chain A: L.18, H.19, M.62, S.63, T.75, E.77, H.78, I.102, T.190, F.191, I.197, L.200, R.201, A.206, G.209, S.210, A.214, V.216, H.237, D.241, H.264 Ligands: ZN.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.18, A:T.190, A:I.197, A:I.197, A:L.200, A:A.206, A:A.214, A:V.216 Hydrogen bonds: A:E.77, A:R.201 Water bridges: A:K.238 pi-Cation interactions: A:R.201

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: A.84, G.85, F.152, S.177, F.181, I.294, S.295, Y.296 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.85, A:S.177 GOL.4: 9 residues within 4Å: Chain A: A.84, F.152, I.243, L.246, Y.247, N.251, S.252, L.253 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.243, A:N.251, A:L.253

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

SO4.5: 4 residues within 4Å: Chain A: D.141, R.143, F.260 Ligands: W8P.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.143 Salt bridges: A:R.143

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: H.78, H.237, D.241 Ligands: W4P.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:H.237, A:D.241, A:D.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuya, T. et al., N-Hydroxyformamide LpxC inhibitors, their in vivo efficacy in a mouse Escherichia coli infection model, and their safety in a rat hemodynamic assay. Bioorg.Med.Chem. (2020)

Release Date

2020-11-25

Peptides

UDP-3-O-acyl-N-acetylglucosamine deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

UDP-3-O-acyl-N-acetylglucosamine deacetylase

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