Research workbench
Crystal structure of bace-1 in complex with inhibitor
Analyse Crystal structure of bace-1 in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CKR
- Type
- protein
- Length
- 1,133 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 009
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 379 | 13% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 13% helix, 38% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 13% helix, 39% strand | P56817 |
Ligands and binding sites
- 009 · (4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-2-oxoimidazolidine-4-carboxamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.75 | 0.85 | 31 | empty |
| 2 | 523 | 0.70 | 0.80 | 64 | 009 |
| 3 | 499 | 0.68 | 0.79 | 58 | 009 |
| 4 | 425 | 0.65 | 0.78 | 43 | 009 |
| 5 | 190 | 0.56 | 0.80 | 37 | empty |
Interfaces
2 interfaces between chains.
- B–C · 785 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 690 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 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 3CKR · PDBe 3CKR · UniProt P56817
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.