Bace-1 incomplex with (7AR)-7A-(5-cyanothiophen-2-yl)-6-(5-fluoro-4- methoxy-6-methylpyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-PYRROLO[3, 4-D]PYRIMIDIN-2-iminium

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).

Ligands and binding sites

• 60V · 5-[(2E,4aR,7aR)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophene-2-carbonitrile · ligand · 2 copies · chains A, B
• TLA · L(+)-tartaric acid · additive · chains 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, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 287 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 5HDV · BACE-1 incomplex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methoxy-6-methylpyrimi… · 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 5HDV · PDBe 5HDV · UniProt P56817