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 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4U4S, 4U4X

  • 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 impact of the position of the nitrogen atom on their binding mode at the AMPA receptors ...

    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: 
    • 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
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2,Glutamate receptor 2A, B263Rattus norvegicusMutation(s): 2 
Gene Names: Gria2Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3C2 (Subject of Investigation/LOI)
Query on 3C2

Download Ideal Coordinates CCD File 
C [auth A], M [auth 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
GLU
Query on GLU

Download Ideal Coordinates CCD File 
F [auth A], Q [auth B]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth A], L [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], N [auth B], O [auth B], P [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A], R [auth B], S [auth B], T [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3C2 Binding MOAD:  4U4X Kd: 9800 (nM) from 1 assay(s)
BindingDB:  4U4X Kd: 9800 (nM) from 1 assay(s)
EC50: min: 5.06e+4, max: 5.06e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.29α = 90
b = 121.569β = 90
c = 47.36γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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