DB00843 : donepezil

Approved drug donepezil ... 2 targets DB00843

Generic name: donepezil PDB Het Group: E20
8 structures in PDB
Brand name(s): aricept, aricept odt, eranz.
Formula: C24H29No3
IUPAC Formula: 2-[(1-Benzylpiperidin-4-Yl)methyl]-5,6-Dimethoxy-2,3-Dihydro-1h-Inden-1-One
PDB name: 1-Benzyl-4-[(5,6-Dimethoxy-1-Indanon-2-Yl)methyl]piperidine

There are 2 target proteins defined in DrugBank for this drug.
1 of these target proteins has one or more structures in the PDB.
There is 1 PDB structure of the drug molecule bound to its target protein.
There are 3 PDB structures containing the drug molecule bound to a protein that is not specified as a target.
KEGG drug
Ligand Expo


Target proteins

DrugBank drug Target 1:   UniProt id: P22303 (ACES_HUMAN)  -  Acetylcholinesterase
UniProt id: P22303    613 a.a.  
4ey7 A,B   530 a.a. 530   X-ray 2.35 Å
The PDB contains 1 entry of donepezil bound to this target protein and 16 entries of this target protein in all (click on orange, plus icon for list).
DrugBank drug Target 2:   UniProt id: P28223 (5HT2A_HUMAN)  -  5-hydroxytryptamine 2A receptor
UniProt id: P28223    471 a.a.  
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)

Key:    PfamA domain  PfamB domain  Secondary structure  Bound drug molecule


Other proteins with donepezil bound in the PDB

There are 2 "non-target" proteins in the PDB containing the donepezil molecule bound. That is, the UniProt code for the proteins is missing or does not match any of the drug targets listed above.

Protein 1:   UniProt id: P04058 ()  -  Acetylcholinesterase OS=Torpedo californica GN=ache PE=1 SV=2
UniProt id: P04058    585 a.a.  
1eve A   534 a.a. 534   X-ray 2.50 Å
The PDB contains 1 entry of donepezil bound to this protein
Protein 2:   Theoretical model of (r)-e2020 bound acetylcholinesterase complex, 3 structures
  No Pfam domain assignments available for this protein.
1. 3ace     14 a.a. 14   Theor. model
  2. 4ace     14 a.a. 14   Theor. model

Key:    PfamA domain  Secondary structure  Bound drug molecule

The black crosses on the secondary structure diagrams indicate where the PDB and UniProt sequences differ.

Where there is more than one PDB model for a given UniProt sequence, the models are ordered by: 1. decreasing order of similarity to the UniProt sequence, 2. X-ray structures (in order of increasing resolution), NMR structures, and theoretical models. Clicking on any PDB code take you to the corresponding PDBsum page.


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