MolNFT v1 · #86268 · protein
New aminoimidazoles as bace-1 inhibitors: from rational design to ab- lowering in brain
4B1D · Beta-secretase 1: “New aminoimidazoles as bace-1 inhibitors: from rational design to ab- lowering in brain”. X-ray diffraction, 1 ligand (6TG), 2 pockets (best druggability 0.69). MolNFT v1 #86268 on GenesisL1: 3D structure, binding…
- PDB
- 4B1D
- Type
- protein
- Length
- 376 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
- 6TG
- Pockets
- 2 · best druggability 0.69
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 | 376 | 16% helix, 42% strand | P56817 |
Ligands and binding sites
- 6TG · (2S)-2-(4-methoxy-3,5-dimethylphenyl)-5-methyl-2-(3-pyrimidin-5-ylphenyl)-2H-imidazol-4-amine · ligand · chains A
- ACT · Acetate ion · additive · 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 | 668 | 0.69 | 0.77 | 65 | ACT, 6TG |
| 2 | 62 | 0.32 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4B1D · New Aminoimidazoles as BACE-1 Inhibitors: From Rational Design to Ab- lowering in Brain · 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 0.98
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 4B1D · PDBe 4B1D · UniProt P56817
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