MolNFT v1 · #47759 · protein
Potent and selective isophthalamide S2 hydroxyethylamine inhibitor of BACE1
2P83 · Beta-secretase 1: “Potent and selective isophthalamide S2 hydroxyethylamine inhibitor of BACE1”. X-ray diffraction, 2 ligands (MR0, PO4), 9 pockets (best druggability 0.72). MolNFT v1 #47759 on GenesisL1: 3D structure, binding sites…
- PDB
- 2P83
- Type
- protein
- Length
- 1,116 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- MR0, PO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 371 | 15% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 372 | 16% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- MR0 · N~3~-{(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-N~1~,N~1~-dipropylbenzene-1,3,5-tricarboxamide · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.72 | 0.81 | 63 | MR0 |
| 2 | 496 | 0.69 | 0.80 | 72 | MR0 |
| 3 | 353 | 0.66 | 0.81 | 42 | MR0 |
| 4 | 376 | 0.64 | 0.79 | 52 | empty |
| 5 | 357 | 0.60 | 0.77 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1079 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 393 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2P83 · Potent and selective isophthalamide S2 hydroxyethylamine inhibitor of BACE1 · 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 B against A, TM-score 0.99
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 2P83 · PDBe 2P83 · UniProt P56817
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