› 2y66

X-ray diffraction
1.49Å resolution

New 5-Benzylidenethiazolidine-4-one Inhibitors of Bacterial MurD Ligase: Design, Synthesis, Crystal Structures, and Biological Evaluation

Released:
DOI: 10.2210/pdb2y66/pdb
PDB entry 2y66 coloured by chain, front view.
PDB entry 2y66 coloured by chain, side view.
PDB entry 2y66 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
New 5-benzylidenethiazolidin-4-one inhibitors of bacterial MurD ligase: design, synthesis, crystal structures, and biological evaluation.
Zidar N, Tomašić T, Šink R, Kovač A, Patin D, Blanot D, Contreras-Martel C, Dessen A, Premru MM, Zega A, Gobec S, Mašič LP, Kikelj D
Eur J Med Chem 46 5512-23 (2011)
PMID: 21963114

Function and Biology Details

Reaction catalysed: 
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147132 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-N-acetylmuramoylalanine--D-glutamate ligase Chain: A
Molecule details ›
Chain: A
Length: 445 amino acids
Theoretical weight: 47.98 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli DH5[alpha]
UniProt:
  • Canonical: P14900 (Residues: 1-438; Coverage: 100%)
Gene names: JW0086, b0088, murD
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand N04 1 x N04
Ligand DMS 1 x DMS
Ligand SO4 1 x SO4
Ligand SO3 1 x SO3
Ligand CL 1 x CL
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P41
Unit cell:
a: 65.604Å b: 65.604Å c: 134.892Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.187 0.217
Expression system: Escherichia coli DH5[alpha]

Quick links

Citations

9 review citations

Rhodanine as a scaffold in drug discovery: a critical review of its biological activities and mechanisms of target modulation.
Tomašić et al. (2012)
8 more

1 mention without citation

Essential Paralogous Proteins as Potential Antibiotic Multitargets in Escherichia coli.
Hardy CD. (2022)