MolNFT v1 · #96627 · protein
Spirocyclic beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors
4JP9 · Beta-secretase 1: “Spirocyclic beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors”. X-ray diffraction, 2 ligands (1M5, NI), 2 pockets (best druggability 0.68). MolNFT v1 #96627 on GenesisL1: 3D structure…
- PDB
- 4JP9
- Type
- protein
- Length
- 402 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
- 1M5, NI
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 402 | 15% helix, 39% strand | P56817 |
Ligands and binding sites
- 1M5 · (4R)-2'-amino-6-(3-chlorophenyl)-1',2,2-trimethyl-2,3-dihydrospiro[chromene-4,4'-imidazol]-5'(1'H)-one · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.68 | 0.78 | 53 | 1M5 |
| 2 | 62 | 0.30 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4JP9 · Spirocyclic Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors · 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 0.95
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 4JP9 · PDBe 4JP9 · UniProt P56817
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