4U4X

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and BPAM37 at 1.56 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Positive Allosteric Modulators of 2-Amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic Acid Receptors Belonging to 4-Cyclopropyl-3,4-dihydro-2H-1,2,4-pyridothiadiazine Dioxides and Diversely Chloro-Substituted 4-Cyclopropyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides.

Francotte, P.Nrholm, A.B.Deva, T.Olsen, L.Frydenvang, K.Goffin, E.Fraikin, P.de Tullio, P.Challal, S.Thomas, J.Y.Iop, F.Louis, C.Botez-Pop, I.Lestage, P.Danober, L.Kastrup, J.S.Pirotte, B.

(2014) J.Med.Chem. 57: 9539-9553

  • DOI: 10.1021/jm501268r
  • Primary Citation of Related Structures:  
  • Also Cited By: 5ELV

  • PubMed Abstract: 
  • Two 4-ethyl-substituted pyridothiadiazine dioxides belonging to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor positive allosteric modulators were cocrystallized with the GluA2 ligand binding domain in order to decipher the impa ...

    Two 4-ethyl-substituted pyridothiadiazine dioxides belonging to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor positive allosteric modulators were cocrystallized with the GluA2 ligand binding domain in order to decipher the impact of the position of the nitrogen atom on their binding mode at the AMPA receptors. The latter was found to be very similar to that of previously described benzothiadiazine-type AMPA receptor modulators. The affinity of the two compounds for the receptor was determined by isothermal titration calorimetry. Accordingly, the synthesis and biological evaluation of novel 4-cyclopropyl-substituted pyridothiadiazine dioxides was performed and completed with the synthesis of the corresponding chloro-substituted 4-cyclopropyl-3,4-dihydro-2H-benzothiadiazine 1,1-dioxides. The "8-aza" compound 32 was found to be the most potent pyridothiadiazine-type AMPA receptor potentiator in vitro, whereas the 7-chloro-substituted compound 36c emerged as the most promising benzothiadiazine dioxide. Due to proper drug-likeness and low in vivo acute toxicity in mice, 36c was chosen for a more complete preclinical evaluation. The compound was able to easily cross the blood-brain barrier. In an in vivo object recognition test with CD1 mice, oral administration of 36c was found to significantly improve cognition performance at doses as low as 1 mg/kg.


    Related Citations: 
    • Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2.
      Krintel, C.,Frydenvang, K.,Olsen, L.,Kristensen, M.T.,de Barrios, O.,Naur, P.,Francotte, P.,Pirotte, B.,Gajhede, M.,Kastrup, J.S.
      (2012) Biochem. J. 441: 173
    • Synthesis, pharmacological and structural characterization, and thermodynamic aspects of GluA2-positive allosteric modulators with a 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide scaffold.
      Noerholm, A.B.,Francotte, P.,Olsen, L.,Krintel, C.,Frydenvang, K.,Goffin, E.,Challal, S.,Danober, L.,Botez-Pop, I.,Lestage, P.,Pirotte, B.,Kastrup, J.S.
      (2013) J. Med. Chem. 56: 8736


    Organizational Affiliation

    Department of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Avenue de l'Hôpital, 1, B36, B-4000 Liège, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2,Glutamate receptor 2
A, B
263Rattus norvegicusMutation(s): 2 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

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

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
3C2
Query on 3C2

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Download CCD File 
A, B
4-ethyl-3,4-dihydro-2H-pyrido[3,2-e][1,2,4]thiadiazine 1,1-dioxide
C8 H11 N3 O2 S
YUNAWRDISADKIN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3C2Kd: 9800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.290α = 90.00
b = 121.569β = 90.00
c = 47.360γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection