MolNFT v1 · #65551 · protein
Discovery of aminoheterocycles as a novel beta-secretase inhibitor class
3H0B · Beta-secretase 1: “Discovery of aminoheterocycles as a novel beta-secretase inhibitor class”. X-ray diffraction, 1 ligand (B35), 9 pockets (best druggability 0.68). MolNFT v1 #65551 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3H0B
- Type
- protein
- Length
- 1,118 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
- B35
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 372 | 14% helix, 42% strand | P56817 |
| B, C | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 13% helix, 42% strand | P56817 |
Ligands and binding sites
- B35 · 4-[(1S)-1-(3-fluoro-4-methoxyphenyl)-2-(2-methoxy-5-nitrophenyl)ethyl]-1H-imidazol-2-amine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.68 | 0.79 | 52 | B35 |
| 2 | 406 | 0.66 | 0.79 | 54 | B35 |
| 3 | 409 | 0.66 | 0.79 | 53 | B35 |
| 4 | 146 | 0.42 | 0.75 | 26 | empty |
| 5 | 56 | 0.37 | 0.79 | 12 | empty |
Interfaces
2 interfaces between chains.
- B–C · 603 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3H0B · Discovery of aminoheterocycles as a novel beta-secretase inhibitor class · 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 3H0B · PDBe 3H0B · UniProt P56817
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