2W8G

Aplysia californica AChBP bound to in silico compound 35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1021/jm801400g
  • Primary Citation of Related Structures:  

  • 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). A ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E
217Aplysia californicaMutation(s): 0 
Find proteins for Q8WSF8 (Aplysia californica)
Go to UniProtKB:  Q8WSF8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BS2
Query on BS2

Download SDF File 
Download CCD File 
A, D, E
(3-ENDO,8-ANTI)-8-BENZYL-3-(10,11-DIHYDRO-5H-DIBENZO[A,D][7]ANNULEN-5-YLOXY)-8-AZONIABICYCLO[3.2.1]OCTANE
C29 H32 N O
DZOFIEFQFCWGIY-GPOLMCQNSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BS2Ki: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 134.510α = 90.00
b = 173.628β = 90.00
c = 129.119γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-09-28
    Type: Database references, Derived calculations
  • Version 1.3: 2015-03-18
    Type: Data collection