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 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 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 ...

    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.


    Related Citations: 
    • Structural basis for partial agonist action at ionotropic glutamate receptors.
      Jin, R., Banke, T.G., Mayer, M.L., Traynelis, S.F., Gouaux, E.
      (2003) Nat Neurosci 6: 803
    • Mechanism of glutamate receptor desensitization.
      Sun, Y., Olson, R., Horning, M., Armstrong, N., Mayer, M., Gouaux, E.
      (2002) Nature 417: 245

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A, B263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4MP (Subject of Investigation/LOI)
Query on 4MP

Download Ideal Coordinates CCD File 
D [auth A]1-(4-METHOXYBENZOYL)-2-PYRROLIDINONE
C12 H13 N O3
ZXNRTKGTQJPIJK-UHFFFAOYSA-N
 Ligand Interaction
FWD (Subject of Investigation/LOI)
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FWD BindingDB:  2AL5 Ki: min: 4, max: 1.00e+4 (nM) from 8 assay(s)
EC50: min: 380, max: 2.09e+4 (nM) from 6 assay(s)
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