Discovery of novel peptidomimetic boronate clpp inhibitors with noncanonical enzyme mechanism as potent virulence blockers in vitro and in vivo

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 25% strand (DSSP).

Ligands and binding sites

• FN3 · [(1S)-3-methyl-1-[[(2S)-3-phenyl-2-(pyrazin-2-ylcarbonylamino)propanoyl]amino]butyl]boronic acid · ligand · 14 copies · chains E, A, B, C, D, F, G, H, I, J, K, L, M, N

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Interfaces

35 interfaces between chains.

• J–K · 1291 Ų buried · 15 hydrogen bonds · protein-protein
• H–I · 1266 Ų buried · 10 hydrogen bonds · protein-protein
• K–L · 1263 Ų buried · 13 hydrogen bonds · protein-protein
• H–N · 1262 Ų buried · 14 hydrogen bonds · protein-protein
• C–D · 1260 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 6L40 · Discovery of novel peptidomimetic boronate ClpP inhibitors with noncanonical enzyme… · the same entry in another collection · chain I against I, TM-score 1.00

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 Q2YSF8
• Elsewhere: RCSB PDB 6L40 · PDBe 6L40 · UniProt Q2YSF8