Research workbench
Spr and structural analysis yield insight towards mechanism of inhibition of bace inhibitors.
Analyse Spr and structural analysis yield insight towards mechanism of inhibition of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I0H
- Type
- protein
- Length
- 1,123 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
- 1BL
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 15% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 16% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 1BL · (2R)-5-{[(2S,3R)-4-{[1-(3-tert-butylphenyl)cyclohexyl]amino}-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]amino}-2-hydroxy-5-oxopentanoic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.68 | 0.79 | 52 | 1BL |
| 2 | 416 | 0.66 | 0.79 | 53 | empty |
| 3 | 450 | 0.66 | 0.78 | 37 | 1BL |
| 4 | 428 | 0.65 | 0.78 | 44 | 1BL |
| 5 | 183 | 0.61 | 0.83 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1060 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 388 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4I0H · SPR and structural analysis yield insight towards mechanism of inhibition of BACE… · 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 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 4I0H · PDBe 4I0H · UniProt P56817
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.