Aplysia californica AChBP bound to in silico compound 31

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.3 of the entry. See complete history


Use of Acetylcholine Binding Protein in the Search for Novel Alpha7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X- Ray Analysis.

Ulens, C.Akdemir, A.Jongejan, A.Van Elk, R.Bertrand, S.Perrakis, A.Leurs, R.Smit, A.B.Sixma, T.K.Bertrand, D.De Esch, I.J.

(2009) J Med Chem 52: 2372

  • DOI: https://doi.org/10.1021/jm801400g
  • Primary Citation of Related Structures:  
    2W8F, 2W8G, 2Y7Y

  • PubMed Abstract: 

    Acetylcholine binding protein (AChBP) is widely considered as a functional and structural homologue of the ligand binding domain of Cys-loop receptors. We report the use of AChBP as template to identify ligands for the nicotinic receptors (nAChRs). An in silico screening protocol was set up and applied to crystal structures of AChBP. Several ligands containing a dibenzosuberyl moiety were identified and shown to bind with high affinity to AChBP and alpha7 nAChRs. Two high affinity ligands were cocrystallized with AChBP, revealing the binding mode in the orthosteric site. Functional studies revealed that these two ligands caused inhibition of the alpha7, alpha4beta2, and 5HT(3) receptors. The noncompetive blockade of the receptors suggests that these compounds act by steric hindrance of the channel. The analysis of the dual binding mode of these dibenzosuberyl-containing compounds can lead to better understanding of the complex mode of action of similar tricyclic ligands on Cys-loop receptors.

  • Organizational Affiliation

    Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
217Aplysia californicaMutation(s): 0 
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BS1

Download Ideal Coordinates CCD File 
K [auth A],
L [auth F]
C24 H30 N O
Binding Affinity Annotations 
IDSourceBinding Affinity
BS1 PDBBind:  2W8F Ki: 500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.8α = 90
b = 76.8β = 90
c = 725.52γ = 120
Software Package:
Software NamePurpose
EVAL15data reduction
EVAL15data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.2: 2011-09-28
    Changes: Database references
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description