Research workbench
8-tetrahydropyran-2-yl chromans: highly selective beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors
Analyse 8-tetrahydropyran-2-yl chromans: highly selective beta-site amyloid precursor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R5N
- 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
- 3J9, NI
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 393 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- 3J9 · (4R,4a'S,10a'R)-8'-(2-fluoropyridin-3-yl)-4a'-methyl-3',4',4a',10a'-tetrahydro-2'H-spiro[1,3-oxazole-4,10'-pyrano[3,2-b]chromen]-2-amine · 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 | 443 | 0.63 | 0.77 | 40 | 3J9 |
| 2 | 62 | 0.34 | 0.77 | 16 | empty |
| 3 | 67 | 0.32 | 0.75 | 17 | empty |
| 4 | 65 | 0.29 | 0.74 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4R5N · 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 4R5N · PDBe 4R5N · UniProt P56817
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