MolNFT v1 · #105578 · protein
Bace-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((R)-1-(2- CYCLOPENTYLACETYL)PYRROLIDIN-3-YL)METHYL)-1-methyl-5-oxoimidazolidin- 2-iminium
4R8Y · Beta-secretase 1: “Bace-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((R)-1-(2…”. X-ray diffraction, 1 ligand (3KO), 7 pockets (best druggability 0.65). MolNFT v1 #105578 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4R8Y
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 3KO
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 16% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 3KO · (2E,5R)-5-(2-cyclohexylethyl)-5-{[(3R)-1-(cyclopentylacetyl)pyrrolidin-3-yl]methyl}-2-imino-3-methylimidazolidin-4-one · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains B
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 | 479 | 0.65 | 0.77 | 42 | 3KO |
| 2 | 449 | 0.64 | 0.77 | 38 | 3KO |
| 3 | 74 | 0.58 | 0.89 | 25 | empty |
| 4 | 73 | 0.56 | 0.87 | 26 | empty |
| 5 | 86 | 0.52 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 293 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4R8Y · BACE-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((R)-1-(2-cyclopentylacetyl)pyrrolidin… · the same entry in another collection · chain B against B, 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 1.00
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 4R8Y · PDBe 4R8Y · UniProt P56817
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