Research workbench
Crystal structure of the bace complex with BDF488, a macrocyclic inhibitor
Analyse Crystal structure of the bace complex with BDF488, a macrocyclic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F3F
- Type
- protein
- Length
- 1,129 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
- AXF
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 40% strand | P56817 |
| B, C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- AXF · (2R,4S)-N-butyl-4-hydroxy-2-methyl- 4-((E)-(4as,12r, 15s,17as)-15-methyl -14,17-dioxo-2,3,4,4A,6,9,11,12, 13, 14,15,16,17,17A-tetradecahydro-1H-5 ,10-dithia-1, 13,16-triaza-benzocycl opentadecen-12-yl)-butyramide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.73 | 0.82 | 66 | AXF |
| 2 | 385 | 0.67 | 0.80 | 44 | AXF |
| 3 | 412 | 0.67 | 0.80 | 45 | AXF |
| 4 | 162 | 0.60 | 0.83 | 37 | empty |
| 5 | 117 | 0.50 | 0.80 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1032 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 440 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 2F3F · Crystal Structure of the Bace complex with BDF488, a macrocyclic 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 A 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 2F3F · PDBe 2F3F · UniProt P56817
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