MolNFT v1 · #99240 · protein
Crystal structure of human beta secretase in complex with compound 12A
4LXM · Beta-secretase 1: “Crystal structure of human beta secretase in complex with compound 12A”. X-ray diffraction, 1 ligand (1YU), 8 pockets (best druggability 0.73). MolNFT v1 #99240 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4LXM
- Type
- protein
- Length
- 1,135 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 1YU
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- 1YU · (1S,3S,4S,5R)-3-{4-amino-3-fluoro-5-[(1,1,1,3,3,3-hexafluoropropan-2-yl)oxy]benzyl}-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1-oxide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.73 | 0.80 | 79 | 1YU |
| 2 | 606 | 0.71 | 0.79 | 67 | 1YU |
| 3 | 502 | 0.70 | 0.80 | 59 | 1YU |
| 4 | 150 | 0.57 | 0.82 | 29 | empty |
| 5 | 151 | 0.43 | 0.75 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1078 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 536 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 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 4LXM · PDBe 4LXM · UniProt P56817
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