SMTL ID : 5vwm.1

Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x C90: N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide(Non-covalent)

C90.1: 19 residues within 4Å: Chain A: L.115, M.159, E.174, H.175, T.287, F.288, M.291, I.294, L.297, A.303, G.306, S.307, A.311, V.313, H.334, K.335, D.338, H.361 Ligands: ZN.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.115, A:F.288, A:I.294, A:I.294, A:L.297, A:A.311, A:V.313 Hydrogen bonds: A:M.159, A:E.174, A:T.287, A:K.335 Water bridges: A:M.159, A:M.159, A:K.335, A:H.361, A:H.361

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.175, T.287, H.334, D.338 Ligands: C90.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.175, A:H.334, A:D.338, A:D.338

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: K.239, G.360, A.362, L.363 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.156, T.158 Ligands: EDO.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.156, A:T.158, A:T.158, H2O.4, H2O.7

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: G.205, V.208, F.209, S.283, R.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.209, A:S.283, A:S.283 EDO.6: 8 residues within 4Å: Chain A: H.116, E.156, T.158, M.159, S.160, D.171, L.302 Ligands: CA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.160, A:S.160 Water bridges: A:T.158, A:T.158, A:T.158, A:T.158, A:T.162 EDO.7: 2 residues within 4Å: Chain A: E.235, G.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.235, A:G.237 Water bridges: A:E.235, A:E.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delker, S.L. et al., Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor. to be published

Release Date

2017-06-07

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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