Research workbench
Crystal structure of BACE1 in complex with hydroxyethylamine- macrocyclic inhibitor 13
Analyse Crystal structure of BACE1 in complex with hydroxyethylamine- macrocyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KE0
- Type
- protein
- Length
- 1,121 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
- 1R8, SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 15% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 372 | 15% helix, 41% strand | P56817 |
Ligands and binding sites
- 1R8 · (3S)-3-[(1R)-2-{[(4S)-6-ethyl-3,4-dihydrospiro[chromene-2,1'-cyclobutan]-4-yl]amino}-1-hydroxyethyl]-4-azabicyclo[10.3.1]hexadeca-1(16),12,14-trien-5-one · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.70 | 0.78 | 80 | 1R8 |
| 2 | 414 | 0.68 | 0.80 | 44 | 1R8 |
| 3 | 401 | 0.67 | 0.80 | 46 | 1R8 |
| 4 | 125 | 0.55 | 0.83 | 29 | empty |
| 5 | 133 | 0.53 | 0.81 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 462 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 457 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4KE0 · Crystal structure of BACE1 in complex with hydroxyethylamine-macrocyclic inhibitor 13 · 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 C against A, TM-score 0.99
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 4KE0 · PDBe 4KE0 · UniProt P56817
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.