Research workbench
Crystal structure of BACE1 in complex with hydroxyethylamine inhibitor 37
Analyse Crystal structure of BACE1 in complex with hydroxyethylamine inhibitor 37 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DI2
- Type
- protein
- Length
- 1,121 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
- 0K9
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 16% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 42% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 371 | 15% helix, 41% strand | P56817 |
Ligands and binding sites
- 0K9 · (2R)-N-{(2S,3R)-4-{[(4'S)-6'-(2,2-dimethylpropyl)-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridin]-4'-yl]amino}-3-hydroxy-1-[3-(1,3-thiazol-2-yl)phenyl]butan-2-yl}-2-methoxypropanamide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.72 | 0.80 | 61 | 0K9, GOL |
| 2 | 656 | 0.71 | 0.78 | 59 | 0K9, GOL |
| 3 | 569 | 0.70 | 0.79 | 69 | 0K9, GOL |
| 4 | 271 | 0.50 | 0.74 | 33 | empty |
| 5 | 105 | 0.40 | 0.76 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 447 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 436 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4DI2 · Crystal structure of BACE1 in complex with hydroxyethylamine inhibitor 37 · 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 4DI2 · PDBe 4DI2 · UniProt P56817
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