MolNFT v1 · #75164 · protein
Crystal structure of human beta secretase in complex with BFG356
3PI5 · Beta-secretase 1: “Crystal structure of human beta secretase in complex with BFG356”. X-ray diffraction, 1 ligand (3P5), 7 pockets (best druggability 0.74). MolNFT v1 #75164 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3PI5
- Type
- protein
- Length
- 1,135 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
- 3P5
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- 3P5 · (3S,4S,5R)-3-(3-bromo-4-hydroxybenzyl)-5-[(3-cyclopropylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide · ligand · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.74 | 0.77 | 105 | 3P5 |
| 2 | 506 | 0.72 | 0.81 | 64 | 3P5 |
| 3 | 372 | 0.67 | 0.80 | 41 | 3P5 |
| 4 | 141 | 0.60 | 0.84 | 32 | empty |
| 5 | 164 | 0.55 | 0.81 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1052 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 9 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 3PI5 · PDBe 3PI5 · UniProt P56817
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