MolNFT v1 · #112578 · protein
BACE1 in complex with 8-(3-((1-aminopropan-2-YL)OXY)BENZYL)-4- (cyclohexylamino)-1-(3-fluorophenyl)-1,3,8-TRIAZASPIRO[4.5]DEC-3-en- 2-one
4ZPF · Beta-secretase 1: “BACE1 in complex with 8-(3-((1-aminopropan-2-YL)OXY)BENZYL)-4…”. X-ray diffraction, 1 ligand (4QD), 2 pockets (best druggability 0.65). MolNFT v1 #112578 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4ZPF
- Type
- protein
- Length
- 371 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
- 4QD
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 371 | 16% helix, 42% strand | P56817 |
Ligands and binding sites
- 4QD · 8-(3-{[(2S)-1-aminopropan-2-yl]oxy}benzyl)-4-(cyclohexylamino)-1-(3-fluorophenyl)-1,3,8-triazaspiro[4.5]dec-3-en-2-one · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.65 | 0.78 | 39 | 4QD |
| 2 | 160 | 0.55 | 0.81 | 32 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4ZPF · BACE1 in complex with 8-(3-((1-aminopropan-2-yl)oxy)benzyl)-4-(cyclohexylamino)-1-(3-fluor… · 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 4ZPF · PDBe 4ZPF · UniProt P56817
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