MolNFT v1 · #80994 · protein
Crystal structure of bace with compound 6
3UDK · Beta-secretase 1: “Crystal structure of bace with compound 6”. X-ray diffraction, 2 ligands (095, ZN), 2 pockets (best druggability 0.67). MolNFT v1 #80994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UDK
- Type
- protein
- Length
- 394 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
- 095, ZN
- Pockets
- 2 · best druggability 0.67
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 | 394 | 14% helix, 40% strand | P56817 |
Ligands and binding sites
- 095 · tetrahydro-2H-pyran-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 445 | 0.67 | 0.79 | 52 | 095, PEG |
| 2 | 54 | 0.29 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 3 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 3UDK · PDBe 3UDK · UniProt P56817
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.