Research workbench
Crystal structure of a cycloamide-urethane-derived novel inhibitor bound to human brain memapsin 2 (beta-secretase).
Analyse Crystal structure of a cycloamide-urethane-derived novel inhibitor bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XS7
- Type
- protein
- Length
- 389 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
- MMI
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 14% helix, 40% strand | P56817 |
Ligands and binding sites
- MMI · N-[(4S,5S,7R)-8-({(S)-1-[(benzylamino)oxomethyl]-2-methylpropyl}amino)-5-hydroxy-2,7-dimethyl-8-oxo-oct-4-yl]-(4S,7S)-4 -isopropyl-2,5,9-trioxo-1-oxa-3,6,10-triazacyclohexadecane-7-carboxamide · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.68 | 0.80 | 46 | MMI |
| 2 | 58 | 0.52 | 0.87 | 21 | empty |
| 3 | 54 | 0.27 | 0.74 | 18 | empty |
Compared structures
- 1XS7 · Crystal Structure of a cycloamide-urethane-derived novel inhibitor bound to human brain… · 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 D 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 1XS7 · PDBe 1XS7 · UniProt P56817
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