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Crystal structure of beta-secretase 1 in complex with selective beta-secretase 1 inhibitor
Analyse Crystal structure of beta-secretase 1 in complex with selective beta-secretase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IXJ
- Type
- protein
- Length
- 1,117 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
- 586, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 14% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 371 | 15% helix, 41% strand | P56817 |
Ligands and binding sites
- 586 · N-[4-(1-benzylcarbamoyl-2-methyl-propylcarbamoyl)-1-(3,5-difluoro-phenoxymethyl)-2-hydroxy-4-methoxy-butyl]-5-(methanes ulfonyl-methyl-amino)-N'-(1-phenylethyl)-isophthalamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.74 | 0.80 | 97 | 586 |
| 2 | 421 | 0.72 | 0.83 | 60 | 586 |
| 3 | 333 | 0.71 | 0.84 | 45 | 586 |
| 4 | 275 | 0.49 | 0.73 | 43 | empty |
| 5 | 58 | 0.39 | 0.80 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 440 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3IXJ · Crystal structure of beta-secretase 1 in complex with selective beta-secretase 1 inhibitor · 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 C 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 3IXJ · PDBe 3IXJ · UniProt P56817
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