Research workbench
Bace crystal structure with hydroxy morpholine inhibitor
Analyse Bace crystal structure with hydroxy morpholine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BFW
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- DK7
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 393 | 15% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- DK7 · N-[(1S,2S)-1-[(3R,6R)-6-(cyclohexylmethoxy)morpholin-3-yl]-3-(3,5-difluorophenyl)-1-hydroxypropan-2-yl]acetamide · ligand · 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.66 | 0.79 | 37 | DK7 |
| 2 | 417 | 0.66 | 0.79 | 44 | DK7 |
| 3 | 90 | 0.54 | 0.85 | 31 | empty |
| 4 | 70 | 0.53 | 0.86 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 398 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 6BFW · PDBe 6BFW · UniProt P56817
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