2QS4

Crystal structure of the GluR5 ligand binding core dimer in complex with LY466195 at 1.58 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.

Alushin, G.M.Jane, D.Mayer, M.L.

(2011) Neuropharmacology 60: 126-134

  • DOI: 10.1016/j.neuropharm.2010.06.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The availability of crystal structures for the ligand binding domains of ionotropic glutamate receptors, combined with their key role in synaptic function in the normal and diseased brain, offers a unique selection of targets for pharmaceutical resea ...

    The availability of crystal structures for the ligand binding domains of ionotropic glutamate receptors, combined with their key role in synaptic function in the normal and diseased brain, offers a unique selection of targets for pharmaceutical research compared to other drug targets for which the atomic structure of the ligand binding site is not known. Currently only a few antagonist structures have been solved, and these reveal ligand specific conformational changes that hinder rational drug design. Here we report high resolution crystal structures for three kainate receptor GluK1 antagonist complexes which reveal new and unexpected modes of binding, highlighting the continued need for experimentally determined receptor-ligand complexes.


    Organizational Affiliation

    Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, DHHS, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor, ionotropic kainate 1
A, B, C, D
258Rattus norvegicusMutation(s): 1 
Gene Names: Grik1 (Glur5)
Find proteins for P22756 (Rattus norvegicus)
Go to UniProtKB:  P22756
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
A, D
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
LY5
Query on LY5

Download SDF File 
Download CCD File 
A, B, C, D
(3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid
LY466195
C16 H24 F2 N2 O4
OXQXJYQSWZFDBB-WJTVCTBASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LY5Kd: 38 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 89.241α = 90.00
b = 89.241β = 90.00
c = 330.365γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
SERGUIdata collection
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2012-08-22
    Type: Database references
  • Version 1.3: 2015-08-05
    Type: Non-polymer description
  • Version 1.4: 2017-08-02
    Type: Source and taxonomy