Research workbench
Structure of bace bound to SCH12472
Analyse Structure of bace bound to SCH12472 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KMY
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- D8Y
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 395 | 15% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 15% helix, 39% strand | P56817 |
Ligands and binding sites
- D8Y · 3-[2-(3-chlorophenyl)ethyl]pyridin-2-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.68 | 0.80 | 48 | D8Y |
| 2 | 385 | 0.64 | 0.79 | 45 | D8Y |
| 3 | 84 | 0.56 | 0.87 | 27 | empty |
| 4 | 60 | 0.55 | 0.89 | 25 | empty |
| 5 | 177 | 0.52 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 247 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 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 3KMY · PDBe 3KMY · UniProt P56817
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