6SBT

Structure of GluK1 ligand-binding domain (S1S2) in complex with N-(7-(1H-imidazol-1-yl)-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl benzamide at 2.3 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

N-(7-(1H-Imidazol-1-yl)-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)benzamide, a New Kainate Receptor Selective Antagonist and Analgesic: Synthesis, X-ray Crystallography, Structure-Affinity Relationships, and in Vitro and in Vivo Pharmacology.

Mollerud, S.Hansen, R.B.Pallesen, J.Temperini, P.Pasini, D.Bornholt, J.Nielsen, B.Mamedova, E.Chalupnik, P.Paternain, A.V.Lerma, J.Diaz-delCastillo, M.Andreasen, J.T.Frydenvang, K.Kastrup, J.S.Johansen, T.N.Pickering, D.S.

(2019) ACS Chem Neurosci 10: 4685-4695

  • DOI: 10.1021/acschemneuro.9b00479
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Selective pharmacological tool compounds are invaluable for understanding the functions of the various ionotropic glutamate receptor subtypes. For the kainate receptors, these compounds are few. Here we have synthesized nine novel quinoxaline-2,3-dio ...

    Selective pharmacological tool compounds are invaluable for understanding the functions of the various ionotropic glutamate receptor subtypes. For the kainate receptors, these compounds are few. Here we have synthesized nine novel quinoxaline-2,3-diones with substitutions in the 7-position to investigate the structure-activity relationship at kainate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Compound 11 exhibited the highest binding affinity across GluK1-3 while having selectivity toward kainate vs AMPA receptors. Compound 11 potently inhibited glutamate evoked currents at homomeric GluK1 and GluK3 receptors in HEK293 cells with K b values of 65 and 39 nM, respectively. The binding mode of 11 in the ligand binding domain of GluK1 was investigated by X-ray crystallography, revealing that 11 stabilizes the receptor in an open conformation, consistent with its demonstrated antagonism. Furthermore, 11 was tested for analgesic effects in the mouse tail flick test where it significantly increased tail flick latency at doses where 2,3-dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[ f ]-quinoxaline-7-sulfonamide (NBQX) was ineffective.


    Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, kainate 1A257Rattus norvegicusMutation(s): 1 
Gene Names: Grik1Glur5
Find proteins for P22756 (Rattus norvegicus)
Explore P22756 
Go to UniProtKB:  P22756
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L5H
Query on L5H

Download CCD File 
A
~{N}-[7-imidazol-1-yl-2,3-bis(oxidanylidene)-6-(trifluoromethyl)-4~{H}-quinoxalin-1-yl]benzamide
C19 H12 F3 N5 O3
IOLCYQPDALFXJR-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.275α = 90
b = 89.275β = 90
c = 156.321γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references