5J5I

X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with 4-(2-amino-6-{bis[(pyridin-2-yl)methyl]amino}pyrimidin-4-yl)phenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.326 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Substituted 2-Aminopyrimidines Selective for alpha 7-Nicotinic Acetylcholine Receptor Activation and Association with Acetylcholine Binding Proteins.

Kaczanowska, K.Camacho Hernandez, G.A.Bendiks, L.Kohs, L.Cornejo-Bravo, J.M.Harel, M.Finn, M.G.Taylor, P.

(2017) J. Am. Chem. Soc. 139: 3676-3684

  • DOI: 10.1021/jacs.6b10746
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Through studies with ligand binding to the acetylcholine binding protein (AChBP), we previously identified a series of 4,6-substituted 2-aminopyrimidines that associate with this soluble surrogate of the nicotinic acetylcholine receptor (nAChR) in a ...

    Through studies with ligand binding to the acetylcholine binding protein (AChBP), we previously identified a series of 4,6-substituted 2-aminopyrimidines that associate with this soluble surrogate of the nicotinic acetylcholine receptor (nAChR) in a cooperative fashion, not seen for classical nicotinic agonists and antagonists. To examine receptor interactions of this structural family on ligand-gated ion channels, we employed HEK cells transfected with cDNAs encoding three requisite receptor subtypes: α7-nAChR, α4β2-nAChR, and a serotonin receptor (5-HT3AR), along with a fluorescent reporter. Initial screening of a series of over 50 newly characterized 2-aminopyrimidines with affinity for AChBP showed only two to be agonists on the α7-nAChR below 10 μM concentration. Their unique structural features were incorporated into design of a second subset of 2-aminopyrimidines yielding several congeners that elicited α7 activation with EC50 values of 70 nM and Kd values for AChBP in a similar range. Several compounds within this series exhibit specificity for the α7-nAChR, showing no activation or antagonism of α4β2-nAChR or 5-HT3AR at concentrations up to 10 μM, while others were weaker antagonists (or partial agonists) on these receptors. Analysis following cocrystallization of four ligand complexes with AChBP show binding at the subunit interface, but with an orientation or binding pose that differs from classical nicotinic agonists and antagonists and from the previously analyzed set of 2-aminopyrimidines that displayed distinct cooperative interactions with AChBP. Orientations of aromatic side chains of these complexes are distinctive, suggesting new modes of binding at the agonist-antagonist site and perhaps an allosteric action for heteromeric nAChRs.


    Organizational Affiliation

    Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093-0650, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylcholine-binding protein
A, B, C, D, E, F, G, H, I, J
218Lymnaea stagnalisMutation(s): 0 
Find proteins for P58154 (Lymnaea stagnalis)
Go to UniProtKB:  P58154
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
6GM
Query on 6GM

Download SDF File 
Download CCD File 
A, B, C, E, F, G, I
4-(2-amino-6-{bis[(pyridin-2-yl)methyl]amino}pyrimidin-4-yl)phenol
C22 H20 N6 O
LXSAXBJSZAHFFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.326 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.144α = 90.00
b = 127.011β = 110.49
c = 122.117γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXmodel building
PHASERphasing
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of CaliforniaUnited StatesTRDRP 21FT-0024

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Database references
  • Version 1.3: 2018-02-21
    Type: Structure summary