MolNFT v1 · #105581 · protein
Bace-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((1S,3R)-3- (CYCLOPENTYLAMINO)CYCLOHEXYL)METHYL)-1-methyl-5-oxoimidazolidin-2- iminium
4R91 · Beta-secretase 1: “Bace-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((1S,3R)-3…”. X-ray diffraction, 1 ligand (3KT), 7 pockets (best druggability 0.69). MolNFT v1 #105581 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4R91
- Type
- protein
- Length
- 773 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
- 3KT
- Pockets
- 7 · best druggability 0.69
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 | 386 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 3KT · (2E,5R)-5-(2-cyclohexylethyl)-5-{[(1S,3R)-3-(cyclopentylamino)cyclohexyl]methyl}-2-imino-3-methylimidazolidin-4-one · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, 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 | 493 | 0.69 | 0.79 | 41 | 3KT |
| 2 | 467 | 0.66 | 0.78 | 39 | 3KT |
| 3 | 73 | 0.60 | 0.90 | 25 | empty |
| 4 | 69 | 0.57 | 0.88 | 24 | empty |
| 5 | 76 | 0.52 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 284 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4R91 · BACE-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((1S,3R)-3-(cyclopentylamino)cyclohexy… · 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 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 4R91 · PDBe 4R91 · UniProt P56817
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