Crystal structure of human bace-1 bound to compound 6

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 42% strand (DSSP).

Ligands and binding sites

• 3WP · (4S)-4-(2,4-difluorophenyl)-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine · ligand · chains A
• NA · Sodium ion · metal · 2 copies · chains A
• IOD · Iodide ion · ion · 2 copies · chains A
• GOL · Glycerol · additive · 3 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 4X2L · Crystal structure of human BACE-1 bound to Compound 6 · 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 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 P56817
• Elsewhere: RCSB PDB 4X2L · PDBe 4X2L · UniProt P56817