MolNFT v1 · #94566 · protein
Spr and structural analysis yield insight towards mechanism of inhibition of bace inhibitors.
4I0H · Beta-secretase 1: “Spr and structural analysis yield insight towards mechanism of inhibition of bace inhibitors.”. X-ray diffraction, 1 ligand (1BL), 13 pockets (best druggability 0.68). MolNFT v1 #94566 on GenesisL1: 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
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