Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5217 at 1.50 A resolution

Experimental Data Snapshot

  • Resolution: 1.49 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Distinct structural features of cyclothiazide are responsible for effects on peak current amplitude and desensitization kinetics at iGluR2.

Hald, H.Ahring, P.K.Timmermann, D.B.Liljefors, T.Gajhede, M.Kastrup, J.S.

(2009) J Mol Biol 391: 906-917

  • DOI: 10.1016/j.jmb.2009.07.002
  • Primary Citation of Related Structures:  
    3H6T, 3H6U, 3H6V, 3H6W

  • PubMed Abstract: 
  • Ionotropic glutamate receptors (iGluRs) mediate fast excitatory neurotransmission. Upon glutamate application, 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid receptors undergo rapid and almost complete desensitization that can be attenuate ...

    Ionotropic glutamate receptors (iGluRs) mediate fast excitatory neurotransmission. Upon glutamate application, 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid receptors undergo rapid and almost complete desensitization that can be attenuated by positive allosteric modulators. The molecular mechanism of positive allosteric modulation has been elucidated previously by crystal structures of the ligand-binding core of iGluR2 in complex with, for example, cyclothiazide (CTZ). Here, we investigate the structure and function of CTZ and three closely related analogues NS1493, NS5206, and NS5217 at iGluR2, by X-ray crystallography and fast application patch-clamp electrophysiology. CTZ was the most efficacious and potent modulator of the four compounds on iGluR2(Q)(i) [E(max) normalized to response of glutamate: 754% (CTZ), 490% (NS1493), 399% (NS5206), and 476% (NS5217) and EC(50) in micromolar: 10 (CTZ), 26 (NS1493), 43 (NS5206), and 48 (NS5217)]. The four modulators divide into three groups according to efficacy and desensitization kinetics: (1) CTZ increases the peak current efficacy twice as much as the three analogues and nearly completely blocks receptor desensitization; (2) NS5206 and NS5217 have low efficacy and only attenuate desensitization partially; (3) NS1493 has low efficacy but nearly completely blocks receptor desensitization. A hydrophobic substituent at the 3-position of the 1,1-dioxo-3,4-dihydro-2H-benzo[e][1,2,4]thiadiazine ring system is important for compound efficacy, with the following ranking: norbornenyl (bicyclo[2.2.1]hept-2-ene)>cyclopentyl>methyl. The replacement of the norbornenyl moiety with a significantly less hydrophobic cyclopentane ring increases the flexibility of the modulator as the cyclopentane ring adopts various conformations at the iGluR2 allosteric binding site. The main structural feature responsible for a nearly complete block of desensitization is the presence of an NH hydrogen bond donor in the 4-position of the 1,1-dioxo-3,4-dihydro-2H-benzo[e][1,2,4]thiadiazine ring system, forming an anchoring hydrogen bond to Ser754. Therefore, the atom at the 4-position of CTZ seems to be a major determinant of receptor desensitization kinetics.

    Related Citations: 
    • 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
    • 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 Medicinal Chemistry, University of Copenhagen, Denmark.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2AB263Rattus norvegicusMutation(s): 1 
Gene Names: Gria2Glur2
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on NS7

Download CCD File 
A, B
(3R)-3-cyclopentyl-6-methyl-7-[(4-methylpiperazin-1-yl)sulfonyl]-3,4-dihydro-2H-1,2-benzothiazine 1,1-dioxide
C19 H29 N3 O4 S2
 Ligand Interaction
Query on GLU

Download CCD File 
A, B
C5 H9 N O4
 Ligand Interaction
Query on SO4

Download CCD File 
A, B
O4 S
 Ligand Interaction
Query on GOL

Download CCD File 
C3 H8 O3
 Ligand Interaction
Query on DMS

Download CCD File 
C2 H6 O S
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLEC50:  71000   nM  BindingDB
GGLKi:  940   nM  BindingDB
GGLEC50:  2190   nM  BindingDB
GGLEC50:  1300   nM  BindingDB
GGLEC50:  21200   nM  BindingDB
GGLEC50:  17000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLKi:  1360   nM  BindingDB
GGLKi:  7400   nM  BindingDB
GGLEC50:  14700   nM  BindingDB
GGLEC50:  19600   nM  BindingDB
GGLEC50:  20000   nM  BindingDB
GGLEC50:  190000   nM  BindingDB
GGLKi:  500   nM  BindingDB
GGLEC50:  52000   nM  BindingDB
GGLKi:  89   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLKi:  280   nM  BindingDB
GGLKi:  282   nM  BindingDB
GGLEC50:  6200   nM  BindingDB
GGLEC50:  35000   nM  BindingDB
GGLKi:  62   nM  BindingDB
GGLEC50:  100000   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLEC50:  22000   nM  BindingDB
GGLEC50:  67000   nM  BindingDB
GGLEC50:  3660   nM  BindingDB
GGLKi:  354   nM  BindingDB
GGLKi:  336   nM  BindingDB
GGLEC50:  2260   nM  BindingDB
GGLEC50:  14000   nM  BindingDB
GGLKi:  249   nM  BindingDB
GGLKi:  254   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Resolution: 1.49 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.01α = 90
b = 47.179β = 91.88
c = 118.412γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-01
    Changes: Refinement description