Crystal structure of a complex between hydroxyethylene inhibitor cp- 108,420 and yeast aspartic proteinase a

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 43% strand (DSSP).

Ligands and binding sites

• 2Y2 · N-[(2R)-1-{[(2S,3R,5R)-1-cyclohexyl-3-hydroxy-5-{[2-(morpholin-4-yl)ethyl]carbamoyl}oct-7-yn-2-yl]amino}-3-(methylsulfa nyl)-1-oxopropan-2-yl]-1H-benzimidazole-2-carboxamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
• BGC · beta-D-glucopyranose · sugar · 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, 1 with a druggability of 0.5 or more.

Modifications

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

Compared structures

• 1FQ4 · Crystal structure of a complex between hydroxyethylene inhibitor cp-108,420 and yeast… · the same entry in another collection · chain A against A, TM-score 1.00
• P07267 · AlphaFold monomer V2.0 prediction for saccharopepsin (P07267) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P07267
• Elsewhere: RCSB PDB 1FQ4 · PDBe 1FQ4 · UniProt P07267