A modular route to novel potent and selective inhibitors of rhomboid intramembrane proteases

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).

Ligands and binding sites

• BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A
• ACE · Acetyl group · ligand · chains C
• W6Q · (2~{R},3~{S})-3-azanyl-~{N}-[(2,5-dimethylphenyl) methyl]-2-oxidanyl-butanamide · ligand · chains A, C
• CL · Chloride ion · ion · 2 copies · chains A, C

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

Pockets

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

Interfaces

1 interface between chains.

• A–C · 411 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

• 5MTF · A modular route to novel potent and selective inhibitors of rhomboid intramembrane… · the same entry in another collection · chain A against A, TM-score 1.00
• B7MDQ0 · AlphaFold monomer V2.0 prediction for rhomboid protease glpg (B7MDQ0) · 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 B7MDQ0
• Elsewhere: RCSB PDB 5MTF · PDBe 5MTF · UniProt B7MDQ0