Discovery of selective and potent inhibitors of gram-positive bacterial thymidylate kinase (tmk: compound 41)

Structure

x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).

Ligands and binding sites

• 13Y · 2-(3-chlorophenoxy)-4-{(1R)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid · ligand · 2 copies · chains A, B

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.

Interfaces

1 interface between chains.

• A–B · 1048 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 4HDC · Discovery of Selective and Potent Inhibitors of Gram-positive Bacterial Thymidylate… · the same entry in another collection · chain A against A, TM-score 1.00
• P65249 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P65249) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P65249
• Elsewhere: RCSB PDB 4HDC · PDBe 4HDC · UniProt P65249