MolNFT v1 · #72303 · protein
Bace-1 in complex with ELN380842
3N4L · Beta-secretase 1: “Bace-1 in complex with ELN380842”. X-ray diffraction, 1 ligand (842), 13 pockets (best druggability 0.69). MolNFT v1 #72303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3N4L
- Type
- protein
- Length
- 1,125 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
- 842
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 16% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 14% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 38% strand | P56817 |
Ligands and binding sites
- 842 · N-[(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-({1-[3-(1H-pyrazol-1-yl)phenyl]cyclohexyl}amino)propyl]acetamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.69 | 0.79 | 61 | 842 |
| 2 | 437 | 0.66 | 0.79 | 51 | 842 |
| 3 | 419 | 0.64 | 0.78 | 39 | 842 |
| 4 | 224 | 0.54 | 0.77 | 33 | empty |
| 5 | 107 | 0.54 | 0.83 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 991 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 1 hydrogen bond · 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 3N4L · PDBe 3N4L · UniProt P56817
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