Research workbench
X-ray structure of BACE1 in complex with a bicyclic isoxazoline carboxamide as the P3 ligand
Analyse X-ray structure of BACE1 in complex with a bicyclic isoxazoline carboxamide as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DHC
- 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
- URE, GHJ, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 15% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 380 | 14% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 14% helix, 40% strand | P56817 |
Ligands and binding sites
- URE · Urea · ligand · 4 copies · chains A, B
- GHJ · (3R,3aR,6aS)-N-[(4R,7S,8S,10R,13S)-8-hydroxy-10,17-dimethyl-7-(2-methylpropyl)-5,11,14-trioxo-13-(propan-2-yl)-2-thia-6,12,15-triazaoctadecan-4-yl]hexahydrofuro[3,2-d][1,2]oxazole-3-carboxamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.73 | 0.78 | 88 | GHJ, GOL |
| 2 | 522 | 0.72 | 0.81 | 63 | GHJ |
| 3 | 641 | 0.71 | 0.78 | 68 | GHJ |
| 4 | 144 | 0.52 | 0.80 | 28 | empty |
| 5 | 83 | 0.31 | 0.73 | 20 | empty |
Interfaces
2 interfaces between chains.
- B–C · 469 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6DHC · X-ray structure of BACE1 in complex with a bicyclic isoxazoline carboxamide as the P3… · the same entry in another collection · chain A against A, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 6DHC · PDBe 6DHC · UniProt P56817
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