Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with bms-681889 aka N~1~-butyl-5-cyano- N~3~-((1S,2R)-1-(3,5- difluorobenzyl)-2-hydroxy-3-((3- METHOXYBENZYL)AMINO)PROPYL)-N~1~- methyl-1H-indole-1,3- dicarboxamide

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 39% strand (DSSP).

Ligands and binding sites

• 3HH · N~1~-butyl-5-cyano-N~3~-{(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-N~1~-methyl-1H-indole-1,3-dicarboxamide · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 774 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 3OHH · Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with bms-681889… · the same entry in another collection · chain A against A, TM-score 1.00
• P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · 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 P56817
• Elsewhere: RCSB PDB 3OHH · PDBe 3OHH · UniProt P56817