Structure-based design of a new series of D-glutamic acid-based inhibitors of bacterial murd ligase

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).

Ligands and binding sites

• T04 · 2-[[2-fluoro-5-[[[4-[(Z)-(4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino]methyl]phenyl]carbonylamino]pentanedioic acid · ligand · chains A
• AZI · Azide ion · ion · 4 copies · chains A
• SO4 · Sulfate ion · ion · 4 copies · chains A
• CL · Chloride ion · ion · 3 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Modifications

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

Compared structures

• 2Y68 · Structure-based design of a new series of D-glutamic acid-based inhibitors of bacterial… · 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 2Y68 · PDBe 2Y68 · UniProt P14900