MolNFT v1 · #158479 · protein
BACE1 in complex with a macrocyclic inhibitor
6NV9 · Beta-secretase 1: “BACE1 in complex with a macrocyclic inhibitor”. X-ray diffraction, 2 ligands (L3M, SO4), 7 pockets (best druggability 0.75). MolNFT v1 #158479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NV9
- Type
- protein
- Length
- 1,114 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
- L3M, SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 16% helix, 42% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 370 | 16% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 371 | 15% helix, 41% strand | P56817 |
Ligands and binding sites
- L3M · (3S)-3-hydroxy-N-(2-methylpropyl)-N~2~-{[(4S)-17-[(methylsulfonyl)(propyl)amino]-2-oxo-3-azatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15, 17-hexaen-4-yl]methyl}-L-norleucinamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 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 | 752 | 0.75 | 0.80 | 92 | L3M |
| 2 | 731 | 0.70 | 0.77 | 83 | L3M |
| 3 | 307 | 0.66 | 0.81 | 36 | L3M |
| 4 | 93 | 0.59 | 0.87 | 31 | empty |
| 5 | 152 | 0.55 | 0.81 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–B · 480 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 5 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 6NV9 · PDBe 6NV9 · UniProt P56817
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