MolNFT v1 · #91926 · protein
Structure of bace in complex with (S)-4-(3-chloro-5-(5-(prop-1-yn-1- YL)PYRIDIN-3-YL)THIOPHEN-2-yl)-1,4-dimethyl-6-oxotetrahydropyrimidin- 2(1H)-iminium
4FRS · Beta-secretase 1: “Structure of bace in complex with (S)-4-(3-chloro-5-(5-(prop-1-yn-1…”. X-ray diffraction, 1 ligand (0V6), 7 pockets (best druggability 0.66). MolNFT v1 #91926 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4FRS
- 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
- 0V6
- Pockets
- 7 · best druggability 0.66
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 | 386 | 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
- 0V6 · (2Z,6S)-6-{3-chloro-5-[5-(prop-1-yn-1-yl)pyridin-3-yl]thiophen-2-yl}-2-imino-3,6-dimethyltetrahydropyrimidin-4(1H)-one · ligand · 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 | 342 | 0.66 | 0.80 | 40 | 0V6 |
| 2 | 352 | 0.65 | 0.79 | 44 | 0V6 |
| 3 | 75 | 0.59 | 0.89 | 28 | empty |
| 4 | 67 | 0.54 | 0.87 | 26 | empty |
| 5 | 129 | 0.52 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 251 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4FRS · Structure of BACE in complex with (S)-4-(3-chloro-5-(5-(prop-1-yn-1-yl)pyridin-3-yl)thioph… · 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 4FRS · PDBe 4FRS · UniProt P56817
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