5O9A

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L504Y-N775S) in complex with glutamate and BPAM121 at 1.78 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


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:  

  • 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 nitrog ...

    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, EC50 = 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.


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2,Glutamate receptor 2
A, B, C, D
264Rattus norvegicusMutation(s): 2 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

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C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

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A, B, C, D
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
7M6
Query on 7M6

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A, B, C, D
7-chloro-4-(2-fluoroethyl)-2,3-dihydro-1,2,4-benzothiadiazine 1,1-dioxide
C9 H10 Cl F N2 O2 S
PDYLKRWZXXTAQJ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.308α = 90.00
b = 98.408β = 90.53
c = 121.787γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references