MolNFT v1 · #131716 · protein
Crystal structure of bace complex with BMC018
5QCP · Beta-secretase 1: “Crystal structure of bace complex with BMC018”. X-ray diffraction, 1 ligand (E4G), 8 pockets (best druggability 0.74). MolNFT v1 #131716 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QCP
- Type
- protein
- Length
- 1,132 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
- E4G
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 16% helix, 42% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- E4G · (4S)-4-[(1R)-1-hydroxy-2-({[3-(propan-2-yl) phenyl]methyl}amino)ethyl]-19-(2-oxopropoxy)-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22), 7,9,17,19-hexaen-2-one · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.74 | 0.81 | 80 | E4G |
| 2 | 479 | 0.73 | 0.82 | 63 | E4G |
| 3 | 364 | 0.70 | 0.83 | 51 | E4G |
| 4 | 84 | 0.47 | 0.82 | 23 | empty |
| 5 | 120 | 0.47 | 0.79 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1047 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 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 5QCP · PDBe 5QCP · UniProt P56817
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