6ZYU

Structure of the GluA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and BPAM549


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of Thiochroman Dioxide Analogues of Benzothiadiazine Dioxides as New Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors.

Etse, K.S.Dorosz, J.McLain Christensen, K.Thomas, J.Y.Botez Pop, I.Goffin, E.Colson, T.Lestage, P.Danober, L.Pirotte, B.Kastrup, J.S.Francotte, P.

(2021) ACS Chem Neurosci 12: 2679-2692

  • DOI: https://doi.org/10.1021/acschemneuro.1c00255
  • Primary Citation of Related Structures:  
    6ZYU

  • PubMed Abstract: 

    On the basis of the activity of 1,2,4-benzothiadiazine 1,1-dioxides as positive allosteric modulators of AMPA receptors, thiochroman 1,1-dioxides were designed applying the isosteric replacement concept. The new compounds expressed strong modulatory activity on AMPA receptors in vitro , although lower than their corresponding benzothiadiazine analogues. The pharmacokinetic profile of three thiochroman 1,1-dioxides ( 12a , 12b , 12e ) was examined in vivo after oral administration, showing that these compounds freely cross the blood-brain barrier. Structural analysis was achieved using X-ray crystallography after cocrystallization of the racemic compound 12b in complex with the ligand-binding domain of GluA2 (L504Y/N775S). Interestingly, both enantiomers of 12b were found to interact with the GluA2 dimer interface, almost identically to its benzothiadiazine analogue, BPAM344 ( 4 ). The interactions of the two enantiomers in the cocrystal were further analyzed (mapping Hirshfeld surfaces and 2D fingerprint) and compared to those of 4 . Taken together, these data explain the lower affinity on AMPA receptors of thiochroman 1,1-dioxides compared to their corresponding 1,2,4-benzothiadiazine 1,1-dioxides.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2,Glutamate receptor 2
A, B, C
264Rattus norvegicusMutation(s): 2 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QSW (Subject of Investigation/LOI)
Query on QSW

Download Ideal Coordinates CCD File 
GA [auth C],
K [auth A],
Z [auth B]
(4~{R})-4-cyclopropyl-7-fluoranyl-3,4-dihydro-2~{H}-thiochromene 1,1-dioxide
C12 H13 F O2 S
LCGAHPABZOKLPB-SNVBAGLBSA-N
QSZ (Subject of Investigation/LOI)
Query on QSZ

Download Ideal Coordinates CCD File 
FA [auth C],
J [auth A],
Y [auth B]
(4~{S})-4-cyclopropyl-7-fluoranyl-3,4-dihydro-2~{H}-thiochromene 1,1-dioxide
C12 H13 F O2 S
LCGAHPABZOKLPB-JTQLQIEISA-N
GLU (Subject of Investigation/LOI)
Query on GLU

Download Ideal Coordinates CCD File 
EA [auth C],
I [auth A],
X [auth B]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
CAC
Query on CAC

Download Ideal Coordinates CCD File 
F [auth A]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
HA [auth C]
IA [auth C]
JA [auth C]
L [auth A]
M [auth A]
HA [auth C],
IA [auth C],
JA [auth C],
L [auth A],
M [auth A],
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
D [auth A]
E [auth A]
R [auth B]
BA [auth C],
CA [auth C],
D [auth A],
E [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
DA [auth C],
G [auth A],
H [auth A],
V [auth B],
W [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B],
KA [auth C],
O [auth A],
P [auth A],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.324α = 90
b = 163.084β = 90
c = 47.449γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark--
Danish Agency for Science Technology and InnovationDenmark--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description