3BBR

Crystal structure of the iGluR2 ligand binding core (S1S2J-N775S) in complex with a dimeric positive modulator as well as glutamate at 2.25 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural proof of a dimeric positive modulator bridging two identical AMPA receptor-binding sites

Kaae, B.H.Harpsoe, K.Kastrup, J.S.Sanz, A.C.Pickering, D.S.Metzler, B.Clausen, R.P.Gajhede, M.Sauerberg, P.Liljefors, T.Madsen, U.

(2007) Chem Biol 14: 1294-1303

  • DOI: 10.1016/j.chembiol.2007.10.012
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Dimeric positive allosteric modulators of ionotropic glutamate receptors were designed, synthesized, and characterized pharmacologically in electrophysiological experiments. The designed compounds are dimers of arylpropylsulfonamides and have been co ...

    Dimeric positive allosteric modulators of ionotropic glutamate receptors were designed, synthesized, and characterized pharmacologically in electrophysiological experiments. The designed compounds are dimers of arylpropylsulfonamides and have been constructed without a linker. The monomeric arylpropylsulfonamides were derived from known modulators and target the cyclothiazide-binding site at the AMPA receptors. The three stereoisomers--R,R, meso, and S,S--of the two constructed dimers were prepared, and in vitro testing showed the R,R forms to be the most potent stereoisomers. The biarylpropylsulfonamides have dramatically increased potencies, more than three orders of magnitude higher than the corresponding monomers. Dimer (R,R)-2a was cocrystallized with the GluR2-S1S2J construct, and an X-ray crystallographic analysis showed (R,R)-2a to bridge two identical binding pockets on two neighboring GluR2 subunits. Thus, this is biostructural evidence of a homomeric dimer bridging two identical receptor-binding sites.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B
263Rattus norvegicusMutation(s): 1 
Gene Names: Gria2Glur2
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BHY
Query on BHY

Download CCD File 
A
N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dimethanesulfonamide
C20 H28 N2 O4 S2
ZESUARCHWPARIF-HOTGVXAUSA-N
 Ligand Interaction
GLU
Query on GLU

Download CCD File 
A, B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLKi:  280   nM  BindingDB
GGLKi:  282   nM  BindingDB
GGLEC50:  190000   nM  BindingDB
GGLKi:  336   nM  BindingDB
GGLEC50:  17000   nM  BindingDB
GGLKi:  249   nM  BindingDB
GGLKi:  254   nM  BindingDB
GGLEC50:  1300   nM  BindingDB
GGLEC50:  14700   nM  BindingDB
GGLEC50:  21200   nM  BindingDB
GGLEC50:  14000   nM  BindingDB
GGLEC50:  19600   nM  BindingDB
GGLEC50:  20000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLEC50:  71000   nM  BindingDB
GGLKi:  940   nM  BindingDB
GGLEC50:  22000   nM  BindingDB
GGLEC50:  2190   nM  BindingDB
GGLKi:  500   nM  BindingDB
GGLKi:  1360   nM  BindingDB
GGLKi:  7400   nM  BindingDB
GGLKi:  354   nM  BindingDB
GGLEC50:  2260   nM  BindingDB
GGLEC50:  52000   nM  BindingDB
GGLEC50:  3660   nM  BindingDB
GGLEC50:  67000   nM  BindingDB
GGLKi:  62   nM  BindingDB
GGLEC50:  100000   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLEC50:  35000   nM  BindingDB
GGLEC50:  6200   nM  BindingDB
GGLKi:  89   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.08α = 90
b = 121.78β = 90
c = 47.427γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-08-16
    Changes: Data collection, Refinement description, Source and taxonomy