MolNFT v1 · #182621 · protein
Bace-1 in complex with compound #22
7MYU · Beta-secretase 1: “Bace-1 in complex with compound #22”. X-ray diffraction, 2 ligands (ZR7, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #182621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MYU
- Type
- protein
- Length
- 779 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- ZR7, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 390 | 16% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- ZR7 · N-{3-[(4ar,7as)-2-amino-6-(5-fluoropyrimidin-2-yl)-4A, 5,6,7-tetrahydropyrrolo[3,4-d][1,3]thiazin-7A(4H)-yl]-4-fluorophenyl}-5-methoxypyrazine-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.72 | 0.84 | 58 | empty |
| 2 | 501 | 0.68 | 0.79 | 42 | ZR7 |
| 3 | 451 | 0.65 | 0.78 | 39 | ZR7 |
| 4 | 333 | 0.61 | 0.78 | 29 | empty |
| 5 | 95 | 0.59 | 0.87 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 7MYU · PDBe 7MYU · UniProt P56817
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