5OEW

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with glutamate and positive allosteric modulator BPAM538


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides as Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors with Nanomolar Potency.

Goffin, E.Drapier, T.Larsen, A.P.Geubelle, P.Ptak, C.P.Laulumaa, S.Rovinskaja, K.Gilissen, J.Tullio, P.Olsen, L.Frydenvang, K.Pirotte, B.Hanson, J.Oswald, R.E.Kastrup, J.S.Francotte, P.

(2018) J Med Chem 61: 251-264

  • DOI: 10.1021/acs.jmedchem.7b01323
  • Primary Citation of Related Structures:  
    5O9A, 5OEW

  • PubMed Abstract: 
  • We report here the synthesis of 7-phenoxy-substituted 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides and their evaluation as AMPA receptor positive allosteric modulators (AMPApams). The impact of substitution on the phenoxy ring and on the nitrogen atom at the 4-position was examined ...

    We report here the synthesis of 7-phenoxy-substituted 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides and their evaluation as AMPA receptor positive allosteric modulators (AMPApams). The impact of substitution on the phenoxy ring and on the nitrogen atom at the 4-position was examined. At GluA2(Q) expressed in HEK293 cells (calcium flux experiment), the most potent compound was 11m (4-cyclopropyl-7-(3-methoxyphenoxy)-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide, EC 50 = 2.0 nM). The Hill coefficient in the screening and the shape of the dimerization curve in small-angle X-ray scattering (SAXS) experiments using isolated GluA2 ligand-binding domain (GluA2-LBD) are consistent with binding of one molecule of 11m per dimer interface, contrary to most benzothiadiazine dioxides developed to date. This observation was confirmed by the X-ray structure of 11m bound to GluA2-LBD and by NMR. This is the first benzothiadiazine dioxide AMPApam to reach the nanomolar range.


    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

    Organizational Affiliation

    Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège , Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A, B, C264Rattus norvegicusMutation(s): 0 
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9TE (Subject of Investigation/LOI)
Query on 9TE

Download Ideal Coordinates CCD File 
I [auth B], R [auth C]4-cyclopropyl-7-(3-methoxyphenoxy)-2,3-dihydro-1$l^{6},2,4-benzothiadiazine 1,1-dioxide
C17 H18 N2 O4 S
CTMHATKTIDUKBM-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
D [auth A], J [auth B], S [auth C]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C] , E [auth A] , F [auth A] , G [auth A] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , 
AA [auth C], E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
BA [auth C], CA [auth C], H [auth A], Q [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9TE BindingDB:  5OEW EC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.702α = 90
b = 164.374β = 90
c = 47.328γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
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: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references