MolNFT v1 · #100521 · protein
Discovery of 7-thp chromans: BACE1 inhibitors that reduce a-beta in the cns
4N00 · Beta-secretase 1: “Discovery of 7-thp chromans: BACE1 inhibitors that reduce a-beta in the cns”. X-ray diffraction, 2 ligands (2EX, NI), 4 pockets (best druggability 0.68). MolNFT v1 #100521 on GenesisL1: 3D structure, binding sites…
- PDB
- 4N00
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 2EX, NI
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 393 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- 2EX · (4R,4a'S,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1-methyl-3',4',4a',10a'-tetrahydro-1'H-spiro[imidazole-4,10'-pyrano[4,3-b]chromen]-5(1H)-one · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.68 | 0.78 | 44 | 2EX |
| 2 | 66 | 0.37 | 0.78 | 16 | empty |
| 3 | 65 | 0.30 | 0.74 | 18 | empty |
| 4 | 51 | 0.26 | 0.73 | 11 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4N00 · Discovery of 7-THP chromans: BACE1 inhibitors that reduce A-beta in the CNS · 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 0.96
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 4N00 · PDBe 4N00 · UniProt P56817
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