3BKI

Crystal Structure of the GluR2 ligand binding core (S1S2J) in complex with FQX at 1.87 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

6-Azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX) forms an irreversible bond to the active site of the GluR2 AMPA receptor.

Cruz, L.A.Estebanez-Perpina, E.Pfaff, S.Borngraeber, S.Bao, N.Blethrow, J.Fletterick, R.J.England, P.M.

(2008) J Med Chem 51: 5856-5860

  • DOI: https://doi.org/10.1021/jm701517b
  • Primary Citation of Related Structures:  
    3BKI

  • PubMed Abstract: 

    AMPA receptors mediate fast excitatory synaptic transmission and are essential for synaptic plasticity. ANQX, a photoreactive AMPA receptor antagonist, is an important biological probe used to irreversibly inactivate AMPA receptors. Here, using X-ray crystallography and mass spectroscopy, we report that ANQX forms two major products in the presence of the GluR2 AMPAR ligand-binding core (S1S2J). Upon photostimulation, ANQX reacts intramolecularly to form FQX or intermolecularly to form a covalent adduct with Glu705.


  • Organizational Affiliation

    Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, California 94158-2517, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2A [auth P],
B,
C,
D
263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
FQX BindingDB:  3BKI IC50: 7600 (nM) from 1 assay(s)
PDBBind:  3BKI IC50: 7600 (nM) from 1 assay(s)
Binding MOAD:  3BKI IC50: 7600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.34α = 90
b = 92.26β = 90
c = 195.24γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Data collection, Refinement description, Source and taxonomy
  • Version 1.3: 2019-09-04
    Changes: Data collection