MolNFT v1 · #80991 · protein
Crystal structure of bace with compound 1
3UDH · Beta-secretase 1: “Crystal structure of bace with compound 1”. X-ray diffraction, 2 ligands (091, ZN), 2 pockets (best druggability 0.68). MolNFT v1 #80991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UDH
- 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
- 091, ZN
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 394 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- 091 · (3S)-spiro[indole-3,3'-pyrrolidin]-2(1H)-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 6 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 | 481 | 0.68 | 0.79 | 52 | 091, EDO |
| 2 | 56 | 0.28 | 0.74 | 19 | 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 3UDH · PDBe 3UDH · UniProt P56817
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