Research workbench
Bace crystal structure with hydroxy pyrrolidine inhibitor
Analyse Bace crystal structure with hydroxy pyrrolidine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BFD
- Type
- protein
- Length
- 782 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
- DJS
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 393 | 16% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- DJS · 2-{[(2S)-butan-2-yl]amino}-N-{(1R,2S)-1-hydroxy-3-phenyl-1-[(2R)-pyrrolidin-2-yl]propan-2-yl}-6-(methylsulfonyl)pyridine-4-carboxamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.71 | 0.82 | 60 | empty |
| 2 | 313 | 0.68 | 0.83 | 47 | DJS |
| 3 | 322 | 0.68 | 0.82 | 45 | DJS |
| 4 | 334 | 0.63 | 0.79 | 35 | GOL |
| 5 | 87 | 0.53 | 0.85 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 479 Ų buried · 2 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 6BFD · PDBe 6BFD · UniProt P56817
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