2AL5

Crystal structure of the GluR2 ligand binding core (S1S2J) in complex with fluoro-willardiine and aniracetam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Mechanism of positive allosteric modulators acting on AMPA receptors.

Jin, R.Clark, S.Weeks, A.M.Dudman, J.T.Gouaux, E.Partin, K.M.

(2005) J Neurosci 25: 9027-9036

  • DOI: https://doi.org/10.1523/JNEUROSCI.2567-05.2005
  • Primary Citation of Related Structures:  
    2AL4, 2AL5

  • PubMed Abstract: 

    Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such as Alzheimer's disease and show promise in the treatment of depression. Previously, there has been limited understanding of the molecular mechanism of action for AMPA receptor potentiators. Here we present cocrystal structures of the glutamate receptor GluR2 S1S2 ligand-binding domain in complex with aniracetam [1-(4-methoxybenzoyl)-2-pyrrolidinone] or CX614 (pyrrolidino-1,3-oxazino benzo-1,4-dioxan-10-one), two AMPA receptor potentiators that preferentially slow AMPA receptor deactivation. Both potentiators bind within the dimer interface of the nondesensitized receptor at a common site located on the twofold axis of molecular symmetry. Importantly, the potentiator binding site is adjacent to the "hinge" in the ligand-binding core "clamshell" that undergoes conformational rearrangement after glutamate binding. Using rapid solution exchange, patch-clamp electrophysiology experiments, we show that point mutations of residues that interact with potentiators in the cocrystal disrupt potentiator function. We suggest that the potentiators slow deactivation by stabilizing the clamshell in its closed-cleft, glutamate-bound conformation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B
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
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4MP
Query on 4MP

Download Ideal Coordinates CCD File 
D [auth A]1-(4-METHOXYBENZOYL)-2-PYRROLIDINONE
C12 H13 N O3
ZXNRTKGTQJPIJK-UHFFFAOYSA-N
FWD
Query on FWD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID
C7 H8 F N3 O4
DBWPFHJYSTVBCZ-BYPYZUCNSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FWD PDBBind:  2AL5 Ki: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.056α = 90
b = 64.126β = 90.07
c = 107.949γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-02
    Changes: Source and taxonomy
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary