MolNFT v1 · #182619 · protein
Bace-1 in complex with compound #18
7MYR · Beta-secretase 1: “Bace-1 in complex with compound #18”. X-ray diffraction, 2 ligands (ZRD, SO4), 5 pockets (best druggability 0.75). MolNFT v1 #182619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MYR
- Type
- protein
- Length
- 780 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
- ZRD, SO4
- Pockets
- 5 · best druggability 0.75
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 | 391 | 16% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- ZRD · (4aR,7aR)-6-(5-fluoropyrimidin-2-yl)-7a-(1,2-thiazol-5-yl)-4,4a,5,6,7,7a-hexahydropyrrolo[3,4-d][1,3]thiazin-2-amine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 738 | 0.75 | 0.80 | 67 | GOL |
| 2 | 488 | 0.67 | 0.78 | 36 | ZRD |
| 3 | 420 | 0.63 | 0.77 | 37 | ZRD |
| 4 | 77 | 0.58 | 0.88 | 25 | empty |
| 5 | 83 | 0.57 | 0.87 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 482 Ų buried · 2 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 7MYR · PDBe 7MYR · UniProt P56817
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