Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with bms-655295 aka N~3~-((1S,2R)-1- benzyl-2-hydroxy-3-((3- METHOXYBENZYL)AMINO)PROPYL)-N~1~, N~1~-dibutyl-1H-indole-1,3- dicarboxamide

Structure

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

Ligands and binding sites

• 3HF · N~3~-{(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-N~1~,N~1~-dibutyl-1H-indole-1,3-dicarboxamide · ligand · 2 copies · chains A, B
• IOD · Iodide ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 846 Ų buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 3OHF · Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with bms-655295… · 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 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 3OHF · PDBe 3OHF · UniProt P56817