6FAZ | pdb_00006faz

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: 1.40 Å
  • R-Value Free: 
    0.168 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.136 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.138 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.8b00250
  • Primary Citation Related Structures: 
    6FAZ

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

Macromolecule Content 

  • Total Structure Weight: 60.91 kDa 
  • Atom Count: 5,136 
  • Modeled Residue Count: 523 
  • Deposited Residue Count: 528 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B
264Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D45

Query on D45



Download:Ideal Coordinates CCD File
P [auth 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
GLU

Query on GLU



Download:Ideal Coordinates CCD File
N [auth A],
Z [auth B]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
Q [auth B],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
K [auth A],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth B],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
M [auth A],
X [auth B],
Y [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
L [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.168 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.136 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.138 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.206α = 90
b = 121.458β = 90
c = 47.164γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary