MolNFT v1 · #88873 · protein
Crystal structure of human beta secretase in complex with nvp-BXQ490
4D88 · Beta-secretase 1: “Crystal structure of human beta secretase in complex with nvp-BXQ490”. X-ray diffraction, 1 ligand (BXQ), 3 pockets (best druggability 0.67). MolNFT v1 #88873 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4D88
- Type
- protein
- Length
- 375 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
- BXQ
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 16% helix, 42% strand | P56817 |
Ligands and binding sites
- BXQ · (3S,4S,5R)-3-{4-amino-3-fluoro-5-[(2S)-3,3,3-trifluoro-2-hydroxypropyl]benzyl}-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.67 | 0.80 | 45 | BXQ |
| 2 | 134 | 0.47 | 0.78 | 27 | empty |
| 3 | 117 | 0.45 | 0.78 | 23 | 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 4D88 · PDBe 4D88 · UniProt P56817
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