6FAZ

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the positive allosteric modulator TDPAM01 at 1.4 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Enhancing Action of Positive Allosteric Modulators through the Design of Dimeric Compounds.

Drapier, T.Geubelle, P.Bouckaert, C.Nielsen, L.Laulumaa, S.Goffin, E.Dilly, S.Francotte, P.Hanson, J.Pochet, L.Kastrup, J.S.Pirotte, B.

(2018) J. Med. Chem. 61: 5279-5291

  • DOI: 10.1021/acs.jmedchem.8b00250

  • PubMed Abstract: 
  • The present study describes the identification of highly potent dimeric 1,2,4-benzothiadiazine 1,1-dioxide (BTD)-type positive allosteric modulators of the AMPA receptors (AMPApams) obtained by linking two monomeric BTD scaffolds through their respec ...

    The present study describes the identification of highly potent dimeric 1,2,4-benzothiadiazine 1,1-dioxide (BTD)-type positive allosteric modulators of the AMPA receptors (AMPApams) obtained by linking two monomeric BTD scaffolds through their respective 6-positions. Using previous X-ray data from monomeric BTDs cocrystallized with the GluA2 ligand-binding domain (LBD), a molecular modeling approach was performed to predict the preferred dimeric combinations. Two 6,6-ethylene-linked dimeric BTD compounds (16 and 22) were prepared and evaluated as AMPApams on HEK293 cells expressing GluA2 o ( Q) (calcium flux experiment). These compounds were found to be about 10,000 times more potent than their respective monomers, the most active dimeric compound being the bis-4-cyclopropyl-substituted compound 22 [6,6'-(ethane-1,2-diyl)bis(4-cyclopropyl-3,4-dihydro-2 H-1,2,4-benzothiadiazine 1,1-dioxide], with an EC 50 value of 1.4 nM. As a proof of concept, the bis-4-methyl-substituted dimeric compound 16 (EC 50 = 13 nM) was successfully cocrystallized with the GluA2 o -LBD and was found to occupy the two BTD binding sites at the LBD dimer interface.


    Organizational Affiliation

    Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark.,Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM) , ULiège , Quartier Hôpital, Avenue Hippocrate, 15, B36 , B-4000 Liège , Belgium.,Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases , ULiège , B34, Quartier Hôpital, Avenue de l'hôpital, 11 , B-4000 Liège , Belgium.,NAmur MEdicine & Drug Innovation Center (NAMEDIC), NARILIS, UNamur , rue de Bruxelles 61 , B-5000 Namur , Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B
264Rattus norvegicusMutation(s): 0 
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
D45
Query on D45

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B
6,6'-(Ethane-1,2-diyl)bis(4-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide)
C18 H22 N4 O4 S2
PZUOXMWBXQXKJK-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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

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

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.206α = 90.00
b = 121.458β = 90.00
c = 47.164γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release