MolNFT v1 · #120838 · protein
Bace-1 in complex with (7AR)-7A-(4-(3-CYANOPHENYL)THIOPHEN-2-yl)-6-(5- fluoropyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-PYRROLO[3,4- D]PYRIMIDIN-2-iminium
5HD0 · Beta-secretase 1: “Bace-1 in complex with (7AR)-7A-(4-(3-CYANOPHENYL)THIOPHEN-2-yl)-6-(5…”. X-ray diffraction, 1 ligand (60Y), 7 pockets (best druggability 0.64). MolNFT v1 #120838 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HD0
- 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
- 60Y
- Pockets
- 7 · best druggability 0.64
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, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- 60Y · 3-{5-[(2E,4aR,7aR)-6-(5-fluoropyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile · 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 | 0.64 | 0.78 | 38 | 60Y |
| 2 | 397 | 0.62 | 0.77 | 40 | 60Y |
| 3 | 65 | 0.60 | 0.90 | 25 | empty |
| 4 | 79 | 0.59 | 0.89 | 27 | empty |
| 5 | 79 | 0.50 | 0.84 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 273 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5HD0 · BACE-1 in complex with (7aR)-7a-(4-(3-cyanophenyl)thiophen-2-yl)-6-(5-fluoropyrimidin-2-yl… · 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 5HD0 · PDBe 5HD0 · UniProt P56817
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.