Crystal structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 39% strand (DSSP).

Ligands and binding sites

• JJX · (4R)-4-(4-cyanophenyl)-6-methyl-2-oxidanylidene-3-[2-oxidanylidene-2-(4-propan-2-ylpiperazin-1-yl)ethyl]-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidine-5-carbonitrile · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 5A0B · Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone… · the same entry in another collection · chain A against A, TM-score 1.00
• P08246 · AlphaFold monomer V2.0 prediction for neutrophil elastase (P08246) · a predicted model of the same protein · chain A against A, 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 P08246
• Elsewhere: RCSB PDB 5A0B · PDBe 5A0B · UniProt P08246