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 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2P2A

  • 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 discriminating GluR2-4 from GluR1 by its more than 10-fold preference for the former receptor subtypes ...

    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: 
    • 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
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A, B263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MP9 (Subject of Investigation/LOI)
Query on MP9

Download Ideal Coordinates CCD File 
G [auth B]2-AMINO-3-[3-HYDROXY-5-(2-BENZYL-2H-5-TETRAZOLYL)-4-ISOXAZOLYL]-PROPIONIC ACID
C14 H14 N6 O4
ZNMNDDBPIVAUGG-JTQLQIEISA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
E [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MP9 PDBBind:  2P2A Ki: 750 (nM) from 1 assay(s)
Binding MOAD:  2P2A Ki: 750 (nM) from 1 assay(s)
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 = 98.12α = 90
b = 121.98β = 90
c = 47.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata 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: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-16
    Changes: Data collection, Refinement description, Source and taxonomy