5BUU

Crystal structure of the GluA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and BPAM-321 at 2.07 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and Pharmacology of Mono-, Di-, and Trialkyl-Substituted 7-Chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides Combined with X-ray Structure Analysis to Understand the Unexpected Structure-Activity Relationship at AMPA Receptors.

Larsen, A.P.Francotte, P.Frydenvang, K.Tapken, D.Goffin, E.Fraikin, P.Caignard, D.H.Lestage, P.Danober, L.Pirotte, B.Kastrup, J.S.

(2016) Acs Chem Neurosci 7: 378-390

  • DOI: 10.1021/acschemneuro.5b00318

  • PubMed Abstract: 
  • Positive allosteric modulators of 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid (AMPA)-type ionotropic glutamate receptors are promising compounds for treatment of neurological disorders, for example, Alzheimer's disease. Here, we report ...

    Positive allosteric modulators of 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid (AMPA)-type ionotropic glutamate receptors are promising compounds for treatment of neurological disorders, for example, Alzheimer's disease. Here, we report synthesis and pharmacological evaluation of a series of mono-, di-, or trialkyl-substituted 7-chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides, comprising in total 16 new modulators. The trisubstituted compounds 7b, 7d, and 7e revealed potent activity (EC2× = 2.7-4.3 μM; concentration of compound responsible for a 2-fold increase of the AMPA mediated response) as AMPA receptor potentiators in an in vitro cellular fluorescence assay (FLIPR). The 4-cyclopropyl compound 7f was found to be considerably less potent (EC2× = 60 μM), in contrast to previously described 4-monoalkyl-substituted benzothiadiazine dioxides for which the cyclopropyl group constitutes the best choice of substituent. 7b was subjected to X-ray structural analysis in complex with the GluA2 ligand-binding domain. We propose an explanation of the unexpected structure-activity relationship of this new series of mono-, di-, and trialkyl-substituted 1,2,4-benzothiadiazine 1,1-dioxide compounds. The methyl substituent in the 3-position directs the binding mode of the 1,2,4-benzothiadiazine 1,1-dioxide (BTD) scaffold. When a methyl substituent is present in the 3-position of the BTD, additional methyl substituents in both the 2- and 4-positions increase potency, whereas introduction of a 4-cyclopropyl group does not enhance potency of 2,3,4-alkyl-substituted BTDs. A hydrogen bond donor in the 2-position of the BTD is not necessary for modulator potency.


    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.
      Norholm, 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
    • Probing the allosteric modulator binding site of GluR2 with thiazide derivatives.
      Ptak, C.P.,Ahmed, A.H.,Oswald, R.E.
      (2009) Biochemistry 48: 8594


    Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical 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,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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
4V6
Query on 4V6

Download SDF File 
Download CCD File 
A, B
(3R)-7-chloro-2,3,4-trimethyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide
BPAM-321
C10 H13 Cl N2 O2 S
KKDTTWULFNGREK-SSDOTTSWSA-N
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
A, B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.209α = 90.00
b = 122.270β = 90.00
c = 47.652γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection