Crystal structure of rat cathepsin D with (5S)-3-(5,6-dihydro-2H- pyran-3-yl)-1-fluoro- 7-(2-fluoropyridin-3-YL)SPIRO[CHROMENO[2,3- C]PYRIDINE-5,4'-[1,3]OXAZOL]-2'-amine

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 45% strand (DSSP).

Ligands and binding sites

• 3UT · (5S)-3-(5,6-dihydro-2H-pyran-3-yl)-1-fluoro-7-(2-fluoropyridin-3-yl)spiro[chromeno[2,3-c]pyridine-5,4'-[1,3]oxazol]-2'-amine · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 396 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 5UX4 · Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-dihydro-2H-pyran-3-yl)-1-fluoro… · the same entry in another collection · chain A against A, TM-score 1.00
• P24268 · AlphaFold monomer V2.0 prediction for cathepsin D (P24268) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P24268
• Elsewhere: RCSB PDB 5UX4 · PDBe 5UX4 · UniProt P24268