MolNFT v1 · #51836 · protein
Human bace-1 in complex with 3-(ethylamino)-N-((1S,2R)-2-hydroxy-1- (phenylmethyl)-3-(((3-(TRIFLUOROMETHYL)PHENYL)METHYL)AMINO)PROPYL)-5- (2-oxo-1-PYRROLIDINYL)BENZAMIDE
2VJ7 · Beta-secretase 1: “Human bace-1 in complex with 3-(ethylamino)-N-((1S,2R)-2-hydroxy-1…”. X-ray diffraction, 1 ligand (VG6), 2 pockets (best druggability 0.71). MolNFT v1 #51836 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2VJ7
- 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
- VG6
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 370 | 15% helix, 41% strand | P56817 |
Ligands and binding sites
- VG6 · N-[(1S,2R)-1-benzyl-2-hydroxy-3-{[3-(trifluoromethyl)benzyl]amino}propyl]-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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.71 | 0.82 | 61 | VG6 |
| 2 | 116 | 0.46 | 0.79 | 24 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2VJ7 · Human BACE-1 in complex with 3-(ethylamino)-N-((1S,2R)-2-hydroxy-1-(phenylmethyl)-3-(((3-(… · the same entry in another collection · chain A against A, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2VJ7 · PDBe 2VJ7 · UniProt P56817
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