Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with (2S)-2-((3R)-3-acetamido-3-isobutyl-2-oxo-1-pyrrolidinyl)-N- ((1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-2-(1,2,3,4-tetrahydro-3- ISOQUINOLINYL)ETHYL)-4-phenylbutanamide

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).

Ligands and binding sites

• PB8 · (2S)-2-[(3R)-3-(acetylamino)-3-(2-methylpropyl)-2-oxopyrrolidin-1-yl]-N-{(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(3R)-1,2,3,4-tetrahydroisoquinolin-3-yl]propan-2-yl}-4-phenylbutanamide · ligand · 4 copies · chains A, B, D, E

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

Pockets

17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• D–E · 775 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 748 Ų buried · 9 hydrogen bonds · protein-protein
• B–D · 111 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide (disulfide).

Compared structures

• 3SKG · Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with… · the same entry in another collection · chain E against E, TM-score 1.00
• P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain B 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 P56817
• Elsewhere: RCSB PDB 3SKG · PDBe 3SKG · UniProt P56817