MolNFT v1 · #51838 · protein
Human bace-1 in complex with N-((1S,2R)-3-(cyclohexylamino)-2-hydroxy- 1-(PHENYLMETHYL)PROPYL)-3-(ethylamino)-5-(2-oxo-1-pyrrolidinyl) benzamide
2VJ9 · Beta-secretase 1: “Human bace-1 in complex with N-((1S,2R)-3-(cyclohexylamino)-2-hydroxy…”. X-ray diffraction, 1 ligand (VG7), 3 pockets (best druggability 0.67). MolNFT v1 #51838 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VJ9
- Type
- protein
- Length
- 374 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- VG7
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 14% helix, 41% strand | P56817 |
Ligands and binding sites
- VG7 · N-[(1S,2R)-1-benzyl-3-(cyclohexylamino)-2-hydroxypropyl]-3-(ethylamino)-5-(2-oxopyrrolidin-1-yl)benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.67 | 0.83 | 38 | VG7 |
| 2 | 131 | 0.45 | 0.77 | 29 | empty |
| 3 | 102 | 0.43 | 0.78 | 24 | empty |
Modifications
Observed in the structure: 3 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 2VJ9 · PDBe 2VJ9 · UniProt P56817
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