2P2A

X-ray structure of the GluR2 ligand binding core (S1S2J) in complex with 2-Bn-tet-AMPA at 2.26A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A tetrazolyl-substituted subtype-selective AMPA receptor agonist.

Vogensen, S.B.Frydenvang, K.Greenwood, J.R.Postorino, G.Nielsen, B.Pickering, D.S.Ebert, B.Bolcho, U.Egebjerg, J.Gajhede, M.Kastrup, J.S.Johansen, T.N.Clausen, R.P.Krogsgaard-Larsen, P.

(2007) J.Med.Chem. 50: 2408-2414

  • DOI: 10.1021/jm061439q
  • Also Cited By: 5FHO, 5FHN, 5FHM

  • PubMed Abstract: 
  • Replacement of the methyl group of the AMPA receptor agonist 2-amino-3-[3-hydroxy-5-(2-methyl-2H-5-tetrazolyl)-4-isoxazolyl]propionic acid (2-Me-Tet-AMPA) with a benzyl group provided the first AMPA receptor agonist, compound 7, capable of discrimina ...

    Replacement of the methyl group of the AMPA receptor agonist 2-amino-3-[3-hydroxy-5-(2-methyl-2H-5-tetrazolyl)-4-isoxazolyl]propionic acid (2-Me-Tet-AMPA) with a benzyl group provided the first AMPA receptor agonist, compound 7, capable of discriminating GluR2-4 from GluR1 by its more than 10-fold preference for the former receptor subtypes. An X-ray crystallographic analysis of this new analogue in complex with the GluR2-S1S2J construct shows that accommodation of the benzyl group creates a previously unobserved pocket in the receptor, which may explain the remarkable pharmacological profile of compound 7.


    Related Citations: 
    • GluR2 Ligand-Binding Core Complexes: Importance of the Isoxazolol Moiety and 5-Substituent for the Binding Mode of AMPA-type Agonists.
      Kasper, C.,Lunn, M.L.,Liljefors, T.,Gouaux, E.,Egebjerg, J.,Kastrup, J.S.
      (2002) FEBS Lett. 531: 173
    • Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 ligand-binding core
      Hogner, A.,Kastrup, J.S.,Jin, R.,Liljefors, T.,Mayer, M.L.,Egebjerg, J.,Larsen, I.K.,Gouaux, E.
      (2002) J.Mol.Biol. 322: 93
    • Mechanisms for Activation and Antagonism of an AMPA-sensitive Glutamate Receptor: Crystal Structures of the GluR2 ligand binding core
      Armstrong, N.,Gouaux, E.
      (2000) Neuron 28: 165


    Organizational Affiliation

    Department of Medicinal Chemistry, The Faculty of Pharmaceutical Sciences, University of Copenhagen, 2 Universitetsparken, DK-2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B
263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
MP9
Query on MP9

Download SDF File 
Download CCD File 
B
2-AMINO-3-[3-HYDROXY-5-(2-BENZYL-2H-5-TETRAZOLYL)-4-ISOXAZOLYL]-PROPIONIC ACID
3-[5-(2-BENZYL-2H-TETRAZOL-5-YL)-3-HYDROXYISOXAZOL-4-YL]-L-ALANINE; 2-BN-TET-AMPA
C14 H14 N6 O4
ZNMNDDBPIVAUGG-JTQLQIEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MP9Ki: 750 nM BINDINGMOAD
MP9Ki: 750 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.120α = 90.00
b = 121.980β = 90.00
c = 47.200γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
CNSrefinement
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-16
    Type: Data collection, Refinement description, Source and taxonomy