2Y54

Fragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Fragment 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis.

Edink, E.Rucktooa, P.Retra, K.Akdemir, A.Nahar, T.Zuiderveld, O.Van Elk, R.Janssen, E.Van Nierop, P.Van Muijlwijk-Koezen, J.Smit, A.B.Sixma, T.K.Leurs, R.De Esch, I.J.P.

(2011) J.Am.Chem.Soc. 133: 5363

  • DOI: 10.1021/ja110571r
  • Primary Citation of Related Structures:  2Y56, 2Y57, 2Y58

  • PubMed Abstract: 
  • Optimization of fragment hits toward high-affinity lead compounds is a crucial aspect of fragment-based drug discovery (FBDD). In the current study, we have successfully optimized a fragment by growing into a ligand-inducible subpocket of the binding ...

    Optimization of fragment hits toward high-affinity lead compounds is a crucial aspect of fragment-based drug discovery (FBDD). In the current study, we have successfully optimized a fragment by growing into a ligand-inducible subpocket of the binding site of acetylcholine-binding protein (AChBP). This protein is a soluble homologue of the ligand binding domain (LBD) of Cys-loop receptors. The fragment optimization was monitored with X-ray structures of ligand complexes and systematic thermodynamic analyses using surface plasmon resonance (SPR) biosensor analysis and isothermal titration calorimetry (ITC). Using site-directed mutagenesis and AChBP from different species, we find that specific changes in thermodynamic binding profiles, are indicative of interactions with the ligand-inducible subpocket of AChBP. This study illustrates that thermodynamic analysis provides valuable information on ligand binding modes and is complementary to affinity data when guiding rational structure- and fragment-based discovery approaches.


    Organizational Affiliation

    Leiden/Amsterdam Center of Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E
217Aplysia californicaN/A
Find proteins for Q8WSF8 (Aplysia californica)
Go to UniProtKB:  Q8WSF8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
V63
Query on V63

Download SDF File 
Download CCD File 
A, B, C, D, E
[(1R,5S)-8-AZABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE
C14 H17 N O2
AZHSHGVBEAPALY-ITGUQSILSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V63Ki: 5011.9 nM (99) BINDINGDB
V63Kd: 20000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 216.420α = 90.00
b = 216.420β = 90.00
c = 216.420γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance