2WKY

Crystal structure of the ligand-binding core of GluR5 in complex with the agonist 4-AHCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Glutamate Receptor Glur5 Agonist (S)-2-Amino-3-(3-Hydroxy-7,8-Dihydro-6H-Cyclohepta[D]Isoxazol-4-Yl)Propionic Acid and the 8-Methyl Analogue: Synthesis, Molecular Pharmacology, and Biostructural Characterization

Clausen, R.P.Naur, P.Kristensen, A.S.Greenwood, J.R.Strange, M.Brauner-Osborne, H.Jensen, A.A.Nielsen, A.S.Geneser, U.Ringgaard, L.M.Nielsen, B.Pickering, D.S.Brehm, L.Gajhede, M.Krogsgaard-Larsen, P.Kastrup, J.S.

(2009) J.Med.Chem. 52: 4911

  • DOI: 10.1021/jm900565c

  • PubMed Abstract: 
  • The design, synthesis, and pharmacological characterization of a highly potent and selective glutamate GluR5 agonist is reported. (S)-2-Amino-3-((RS)-3-hydroxy-8-methyl-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)propionic acid (5) is the 8-methyl anal ...

    The design, synthesis, and pharmacological characterization of a highly potent and selective glutamate GluR5 agonist is reported. (S)-2-Amino-3-((RS)-3-hydroxy-8-methyl-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)propionic acid (5) is the 8-methyl analogue of (S)-2-amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)propionic acid ((S)-4-AHCP, 4). Compound 5 displays an improved selectivity profile compared to 4. A versatile stereoselective synthetic route for this class of compounds is presented along with the characterization of the binding affinity of 5 to ionotropic glutamate receptors (iGluRs). Functional characterization of 5 at cloned iGluRs using a calcium imaging assay and voltage-clamp recordings show a different activation of GluR5 compared to (S)-glutamic acid (Glu), kainic acid (KA, 1), and (S)-2-amino-3-(3-hydroxy-5-tert-butyl-4-isoxazolyl)propionic acid ((S)-ATPA, 3) as previously demonstrated for 4. An X-ray crystallographic analysis of 4 and computational analyses of 4 and 5 bound to the GluR5 agonist binding domain (ABD) are presented, including a watermap analysis, which suggests that water molecules in the agonist binding site are important selectivity determinants.


    Organizational Affiliation

    Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, 2 Universitetsparken, DK-2100 Copenhagen, Denmark. rac@farma.ku.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
A, B
258Rattus norvegicusMutation(s): 0 
Gene Names: Grik1 (Glur5)
Find proteins for P22756 (Rattus norvegicus)
Go to UniProtKB:  P22756
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IBC
Query on IBC

Download SDF File 
Download CCD File 
A, B
3-(3-HYDROXY-7,8-DIHYDRO-6H-CYCLOHEPTA[D]ISOXAZOL-4-YL)-L-ALANINE
2-AMINO-3-(3-HYDROXY-7,8-DIHYDRO-6H-CYCLOHEPTA[D]-4-ISOXAZOLYL)PROPIONIC ACID
C11 H14 N2 O4
HJEPOXZLPHUVFE-ZETCQYMHSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IBCKi: 2.57 nM BINDINGMOAD
IBCKi: 2.57 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.310α = 90.00
b = 71.310β = 90.00
c = 234.958γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-06-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-09
    Type: Data collection