› 4u3d

X-ray diffraction
1.25Å resolution

LpxC from A.Aaeolicus in complex with 4-[[4-[2-[4-(morpholinomethyl)phenyl]ethynyl]phenoxy]methyl]tetrahydropyran-4-carbohydroxamic acid (compound 9)

Released:
DOI: 10.2210/pdb4u3d/pdb
PDB entry 4u3d coloured by chain, front view.
PDB entry 4u3d coloured by chain, side view.
PDB entry 4u3d coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
Primary publication:
Synthesis, Structure, and SAR of Tetrahydropyran-Based LpxC Inhibitors.
Murphy-Benenato KE, Olivier N, Choy A, Ross PL, Miller MD, Thresher J, Gao N, Hale MR
ACS Med Chem Lett 5 1213-8 (2014)
PMID: 25408833

Function and Biology Details

Reaction catalysed: 
UDP-3-O-((3R)-3-hydroxyacyl)-N-acetyl-alpha-D-glucosamine + H(2)O = UDP-3-O-((3R)-3-hydroxyacyl)-alpha-D-glucosamine + acetate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130526 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-3-O-acyl-N-acetylglucosamine deacetylase Chain: A
Molecule details ›
Chain: A
Length: 271 amino acids
Theoretical weight: 30.99 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O67648 (Residues: 1-271; Coverage: 96%)
Gene names: aq_1772, envA, lpxC
Sequence domains: UDP-3-O-acyl N-acetylglycosamine deacetylase
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand IMD 1 x IMD
Ligand ZN 2 x ZN
Ligand CL 1 x CL
Ligand 3BX 1 x 3BX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P61
Unit cell:
a: 65.865Å b: 65.865Å c: 133.282Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.158 0.158 0.168
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Antibacterial Drug Discovery Targeting the Lipopolysaccharide Biosynthetic Enzyme LpxC.
Erwin AL. (2016)
8 other articles

1 mention without citation

Synthesis, Structure, and SAR of Tetrahydropyran-Based LpxC Inhibitors.
Murphy-Benenato et al. (2014)