Discovery of novel 5-benzylidenerhodanine- and 5-benzylidene- thiazolidine-2,4-dione inhibitors of murd ligase

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).

Ligands and binding sites

• VSV · N-({3-[({4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl}amino)methyl]phenyl}carbonyl)-D-glutamic acid · ligand · chains A
• CL · Chloride ion · ion · 4 copies · chains A
• SO4 · Sulfate ion · ion · 2 copies · chains A
• AZI · Azide ion · ion · chains A
• SO3 · Sulfite ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 1 disulfide, 1 modified (disulfide, carboxylation).

Compared structures

• 2X5O · Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione… · the same entry in another collection · chain A against A, TM-score 1.00
• P14900 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoylalanine-- D-glutamate ligase… · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P14900
• Elsewhere: RCSB PDB 2X5O · PDBe 2X5O · UniProt P14900