MolNFT v1 · #106185 · protein
8-tetrahydropyran-2-yl chromans: highly selective beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors
4RRO · Beta-secretase 1: “8-tetrahydropyran-2-yl chromans: highly selective beta-site amyloid precursor protein cleaving enzyme 1…”. X-ray diffraction, 2 ligands (3UX, NI), 4 pockets (best druggability 0.64). MolNFT v1 #106185 on…
- PDB
- 4RRO
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 3UX, NI
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 393 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 3UX · (4S,4a'R,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1,4a'-dimethyl-3',4',4a',10a'-tetrahydro-2'H-spiro[imidazole-4,10'-pyrano[3,2-b]chromen]-5(1H)-one · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.64 | 0.77 | 43 | 3UX |
| 2 | 74 | 0.38 | 0.78 | 15 | empty |
| 3 | 56 | 0.28 | 0.74 | 16 | empty |
| 4 | 58 | 0.28 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4RRO · 8-Tetrahydropyran-2-yl chromans: highly selective beta-site amyloid precursor protein… · 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 0.96
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 4RRO · PDBe 4RRO · UniProt P56817
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