Structure of cathepsin D with inhibitor 2-bromo-N-[(2S,3S)-4-{[2-(2,4- DICHLOROPHENYL)ETHYL][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl) PROPANOYL]AMINO}-3-hydroxy-1-(3-PHENOXYPHENYL)BUTAN-2-yl]-4,5- dimethoxybenzamide

Structure

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

Ligands and binding sites

• 2S1 · 2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoyl]amino}-3-hydroxy-1-(3-phenoxyphenyl)butan-2-yl]-4,5-dimethoxybenzamide · ligand · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · chains B
• MAN · alpha-D-mannopyranose · sugar · chains B
• GOL · Glycerol · additive · chains A, B

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.

Interfaces

1 interface between chains.

• A–B · 3213 Ų buried · 80 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 4OC6 · Structure of Cathepsin D with inhibitor 2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl… · the same entry in another collection · chain A against A, TM-score 1.00
• P07339 · AlphaFold monomer V2.0 prediction for cathepsin D (P07339) · a predicted model of the same protein · chain B 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 P07339
• Elsewhere: RCSB PDB 4OC6 · PDBe 4OC6 · UniProt P07339