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, 24% strand (DSSP).

Ligands and binding sites

• E4U · [(1~{R})-1-[[(2~{S})-2-[[2,5-bis(chloranyl) phenyl]carbonylamino]-3-(1~{H}-indol-3-yl) propanoyl]amino]-3-methyl-butyl]boronic acid · ligand · 14 copies · chains A, B, C, D, E, 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, 20 with a druggability of 0.5 or more.

Interfaces

35 interfaces between chains.

• B–C · 1389 Ų buried · 16 hydrogen bonds · protein-protein
• A–G · 1388 Ų buried · 14 hydrogen bonds · protein-protein
• C–E · 1384 Ų buried · 17 hydrogen bonds · protein-protein
• J–K · 1358 Ų buried · 13 hydrogen bonds · protein-protein
• M–N · 1353 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6L3X · Discovery of novel peptidomimetic boronate ClpP inhibitors with noncanonical enzyme… · the same entry in another collection · chain K against K, 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 6L3X · PDBe 6L3X · UniProt Q2YSF8