Crystal structure of bace-1 in complex with 5-cyano-pyridine-2- carboxylic acid [3-((4S,6S)-2-amino-4-fluoromethyl-6-trifluoromethyl- 5,6-dihydro-4H-[1,3]OXAZIN-4-yl)-4-fluoro-phenyl]-amide

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).

Ligands and binding sites

• 1HM · N-{3-[(4S,6S)-2-amino-4-(fluoromethyl)-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide · ligand · chains A
• NA · Sodium ion · metal · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 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

• 4J1E · CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-Cyano-pyridine-2-carboxylic acid… · 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 0.98

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 P56817
• Elsewhere: RCSB PDB 4J1E · PDBe 4J1E · UniProt P56817