9SND | pdb_00009snd

Mus musculus acetylcholinesterase in complex with 2-(1H-indol-3-yl)-N-(2-methoxybenzyl)ethan-1-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.223 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Potent and selective indole-based inhibitors targeting disease-transmitting mosquitoes.

Rajeshwari, R.Duvauchelle, V.Lindgren, C.Stangner, K.Knutsson, S.Forsgren, N.Ekstrom, F.Kamau, L.Linusson, A.

(2025) RSC Med Chem 

  • DOI: https://doi.org/10.1039/d5md00797f
  • Primary Citation of Related Structures:  
    9SND, 9SNJ

  • PubMed Abstract: 

    Vector control with insecticides is an important preventive measure against mosquito-borne infectious diseases, such as malaria and dengue. The intensive usage of few insecticides has resulted in emerging resistance in mosquitoes, and unwanted off-target toxic effects. Therefore, there is great interest in alternative active ingredients. Here, we explore indole-based compounds as selective inhibitors against acetylcholinesterase 1 (AChE1) from the disease-transmitting mosquitoes Anopheles gambiae ( An. gambiae , Ag AChE1) and Aedes aegypti ( Ae. aegypti , Ae AChE1) as potential candidates for future insecticides used in vector control. Three sets of compounds were designed to explore their structure-activity relationship, and investigate their potentials regarding potency and selectivity. 26 indole-based compounds were synthesized and biochemically evaluated for inhibition against Ag AChE1, Ae AChE1, and human AChE ( h AChE). The compounds were shown to be potent inhibitors against AChE1, and selective for AChE1 over h AChE. N -Methylation of the indole moiety clearly increased the inhibition potency, and a bulkier benzyl moiety improved the selectivity. X-ray crystallography shows that the inhibitors bind at the bottom of the active site gorge of mouse AChE ( m AChE), while molecular dynamics simulations revealed different binding poses in m AChE and Ag AChE1. Four potent and selective inhibitors were subjected to in vivo mosquito testing. Topical application showed strong insecticidal effects on An. gambiae and Ae. aegypti , highlighting this compound class as an interesting alternative for future insecticide research.


  • Organizational Affiliation
    • Department of Chemistry, Umeå University Sweden anna.linusson@umu.se.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholinesterase
A, B
543Mus musculusMutation(s): 0 
Gene Names: Ache
EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus)
Explore P21836 
Go to UniProtKB:  P21836
IMPC:  MGI:87876
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21836
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9YU
Query on 9YU

Download Ideal Coordinates CCD File 
D [auth A]2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol
C15 H32 O8
AGWKUHGLWHMYTG-UHFFFAOYSA-N
A1JOW (Subject of Investigation/LOI)
Query on A1JOW

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth B]
2-(1~{H}-indol-3-yl)-~{N}-[(2-methoxyphenyl)methyl]ethanamine
C18 H20 N2 O
HJCSKFSDXDPIKM-UHFFFAOYSA-N
TOE
Query on TOE

Download Ideal Coordinates CCD File 
G [auth A]2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
C7 H16 O4
JLGLQAWTXXGVEM-UHFFFAOYSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
L [auth B]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.353α = 90
b = 111.104β = 90
c = 227.383γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-00664

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-28
    Type: Initial release