MolNFT v1 · #121381 · protein
BACE1 in complex with 4-(3-(furan-2-CARBOXAMIDO)PHENYL)-1-methyl-5- oxo-4-phenylimidazolidin-2-iminium
5HU0 · Beta-secretase 1: “BACE1 in complex with 4-(3-(furan-2-CARBOXAMIDO)PHENYL)-1-methyl-5- oxo-4-phenylimidazolidin-2-iminium”. X-ray diffraction, 1 ligand (66H), 7 pockets (best druggability 0.67). MolNFT v1 #121381 on GenesisL1: 3D…
- PDB
- 5HU0
- Type
- protein
- Length
- 779 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
- 66H
- Pockets
- 7 · best druggability 0.67
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 | 390 | 16% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- 66H · N-{3-[(2E,4R)-2-imino-1-methyl-5-oxo-4-phenylimidazolidin-4-yl]phenyl}furan-2-carboxamide · 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 | 430 | 0.67 | 0.79 | 39 | 66H |
| 2 | 497 | 0.66 | 0.78 | 42 | 66H |
| 3 | 80 | 0.57 | 0.87 | 27 | empty |
| 4 | 88 | 0.53 | 0.84 | 17 | empty |
| 5 | 82 | 0.51 | 0.84 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 272 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5HU0 · BACE1 in complex with 4-(3-(furan-2-carboxamido)phenyl)-1-methyl-5-oxo-4-phenylimidazolidi… · 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 5HU0 · PDBe 5HU0 · UniProt P56817
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