Research workbench
Crystal structure of beta-secretase bond to an inhibitor with isophthalamide derivatives at P2-P3
Analyse Crystal structure of beta-secretase bond to an inhibitor with isophthalamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P4J
- Type
- protein
- Length
- 1,556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 23I
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 15% helix, 38% strand | P56817 |
Ligands and binding sites
- 23I · N-[(1S,2S,4R)-2-hydroxy-1-isobutyl-5-({(1S)-1-[(isopropylamino)carbonyl]-2-methylpropyl}amino)-4-methyl-5-oxopentyl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]isophthalamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.73 | 0.81 | 70 | 23I |
| 2 | 441 | 0.72 | 0.82 | 39 | empty |
| 3 | 512 | 0.71 | 0.80 | 72 | 23I |
| 4 | 491 | 0.71 | 0.80 | 66 | 23I |
| 5 | 434 | 0.70 | 0.81 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–D · 820 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 820 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 195 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2P4J · Crystal structure of beta-secretase bond to an inhibitor with Isophthalamide Derivatives… · the same entry in another collection · chain D against D, 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 0.99
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 2P4J · PDBe 2P4J · UniProt P56817
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