2W8F | pdb_00002w8f

Aplysia californica AChBP bound to in silico compound 31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.267 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/jm801400g
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 247.58 kDa 
  • Atom Count: 16,482 
  • Modeled Residue Count: 2,050 
  • Deposited Residue Count: 2,170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
217Aplysia californicaMutation(s): 0 
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BS1

Query on BS1



Download:Ideal Coordinates CCD File
K [auth A],
L [auth F]
(3-EXO)-3-(10,11-DIHYDRO-5H-DIBENZO[A,D][7]ANNULEN-5-YLOXY)-8,8-DIMETHYL-8-AZONIABICYCLO[3.2.1]OCTANE
C24 H30 N O
BADPXOSJBUEVTR-WKCHPHFGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.267 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
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
REFMACrefinement
EVAL15data reduction
EVAL15data scaling
MOLREPphasing

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
  • Version 1.4: 2024-10-23
    Changes: Structure summary