Research workbench
Bace (beta secretase) in complex with a nanomolar non- peptidic inhibitor
Analyse Bace (beta secretase) in complex with a nanomolar non- peptidic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W51
- Type
- protein
- Length
- 374 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
- L01, IOD
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 14% helix, 40% strand | P56817 |
Ligands and binding sites
- L01 · 3-[({(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}amino)(hydroxy)methyl]-N,N-dipropylbenzamide · ligand · chains A
- IOD · Iodide ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.72 | 0.81 | 63 | L01 |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1W51 · BACE (Beta Secretase) in complex with a nanomolar non-peptidic inhibitor · 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 1W51 · PDBe 1W51 · UniProt P56817
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