Research workbench
Crystal structure of human acetylcholinesterase in complex with donepezil
Analyse Crystal structure of human acetylcholinesterase in complex with donepezil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E3H
- Type
- protein
- Length
- 1,054 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P22303
- Ligands
- E20, NAG, FUC
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylcholinesterase (EC 3.1.1.7) | protein | 527 | 38% helix, 17% strand | P22303 |
Ligands and binding sites
- E20 · 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl) methyl]piperidine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.78 | 0.90 | 36 | E20 |
| 2 | 275 | 0.77 | 0.89 | 38 | E20 |
| 3 | 324 | 0.59 | 0.77 | 35 | empty |
| 4 | 299 | 0.58 | 0.77 | 34 | empty |
| 5 | 139 | 0.57 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7E3H · Crystal structure of human acetylcholinesterase in complex with donepezil · the same entry in another collection · chain A against A, TM-score 1.00
- P22303 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P22303) · a predicted model of the same protein · chain B 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 P22303
- Elsewhere: RCSB PDB 7E3H · PDBe 7E3H · UniProt P22303
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