S.AUREUS tmk in complex with the potent inhibitor compound 38, 2-(3- chlorophenoxy)-3-methoxy-4-{(1R)-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4- dihydropyrimidin-1(2H)-YL)PIPERIDIN-1-YL]PROPYL}BENZOIC acid

Structure

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

Ligands and binding sites

• 32B · 2-(3-chlorophenoxy)-3-methoxy-4-{(1R)-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]propyl}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 · 1031 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 4QGF · S.aureus TMK in complex with the potent inhibitor compound 38… · the same entry in another collection · chain A against A, TM-score 1.00
• Q6GJI9 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q6GJI9) · 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 Q6GJI9
• Elsewhere: RCSB PDB 4QGF · PDBe 4QGF · UniProt Q6GJI9