2Y56

Fragment growing induces conformational changes in acetylcholine- binding protein: A structural and thermodynamic analysis - (Compound 3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    2Y54, 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 site of acetylcholine-binding protein (AChBP) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SOLUBLE ACETYLCHOLINE RECEPTORA, B, C, D, E217Aplysia californicaMutation(s): 0 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V11 (Subject of Investigation/LOI)
Query on V11

Download Ideal Coordinates CCD File 
AA [auth D], F [auth A], KA [auth E], M [auth B], T [auth C][(1S,5R)-8-[(2R)-2-HYDROXY-2-PHENYL-ETHYL]-8-AZABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE
C22 H25 N O3
CAELFFAMXVUOKR-BQJUDKOJSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth D] , FA [auth D] , GA [auth D] , I [auth A] , J [auth A] , NA [auth E] , OA [auth E] , PA [auth E] , 
EA [auth D], FA [auth D], GA [auth D], I [auth A], J [auth A], NA [auth E], OA [auth E], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], W [auth C], X [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
HA [auth D], IA [auth D], JA [auth D], K [auth A], L [auth A], S [auth B], Y [auth C], Z [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , DA [auth D] , G [auth A] , H [auth A] , LA [auth E] , MA [auth E] , N [auth B] , 
BA [auth D], CA [auth D], DA [auth D], G [auth A], H [auth A], LA [auth E], MA [auth E], N [auth B], O [auth B], P [auth B], U [auth C], V [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
V11 BindingDB:  2Y56 Ki: 100 (nM) from 1 assay(s)
PDBBind:  2Y56 Kd: 310 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.93α = 90
b = 218.93β = 90
c = 218.93γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-04-24
    Changes: Data collection, Other, Source and taxonomy