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 5O9A | pdb_00005o9a

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 (Depositor), 0.169 (DCC) 
  • R-Value Work: 
    0.153 (Depositor) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5O9A

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.7b01323
  • Primary Citation 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. 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.


  • 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.

Macromolecule Content 

  • Total Structure Weight: 121.37 kDa 
  • Atom Count: 9,878 
  • Modeled Residue Count: 1,050 
  • Deposited Residue Count: 1,056 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor 2,Glutamate receptor 2
A, B, C, D
264Rattus norvegicusMutation(s): 2 
Gene Names: Gria2, Glur2
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
7M6

Query on 7M6



Download:Ideal Coordinates CCD File
CA [auth C],
I [auth A],
MA [auth D],
S [auth B]
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
CIT

Query on CIT



Download:Ideal Coordinates CCD File
EA [auth C]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
GLU

Query on GLU



Download:Ideal Coordinates CCD File
HA [auth C],
N [auth A],
PA [auth D],
V [auth B]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
GA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
E [auth A]
F [auth A]
G [auth A]
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
IA [auth D],
JA [auth D],
KA [auth D],
LA [auth D],
Q [auth B],
R [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
FA [auth C],
M [auth A],
O [auth A],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
P [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
DA [auth C]
J [auth A]
K [auth A]
L [auth A]
NA [auth D]
DA [auth C],
J [auth A],
K [auth A],
L [auth A],
NA [auth D],
OA [auth D],
T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.179 (Depositor), 0.169 (DCC) 
  • R-Value Work:  0.153 (Depositor) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.308α = 90
b = 98.408β = 90.53
c = 121.787γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
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: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary