MolNFT v1 · #51835 · protein
Human bace-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylamino)- 1-methyl-2-OXOETHYL)AMINO)-2-hydroxy-1-(PHENYLMETHYL)PROPYL)-3- (ethylamino)-5-(2-oxo-1-PYRROLIDINYL)BENZAMIDE
2VJ6 · Beta-secretase 1: “Human bace-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylamino)…”. X-ray diffraction, 1 ligand (VG5), 3 pockets (best druggability 0.68). MolNFT v1 #51835 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2VJ6
- Type
- protein
- Length
- 370 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
- VG5
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 370 | 15% helix, 42% strand | P56817 |
Ligands and binding sites
- VG5 · N-[(1S,2R)-1-benzyl-3-{[(1S)-2-(cyclohexylamino)-1-methyl-2-oxoethyl]amino}-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 | 325 | 0.68 | 0.82 | 47 | VG5 |
| 2 | 112 | 0.45 | 0.78 | 26 | empty |
| 3 | 102 | 0.37 | 0.75 | 28 | 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 2VJ6 · PDBe 2VJ6 · UniProt P56817
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