6F29

Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2-Amino-2-carboxyethyl]-5,7-dihydrothieno[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.6A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

( S)-2-Amino-3-(5-methyl-3-hydroxyisoxazol-4-yl)propanoic Acid (AMPA) and Kainate Receptor Ligands: Further Exploration of Bioisosteric Replacements and Structural and Biological Investigation.

Brogi, S.Brindisi, M.Butini, S.Kshirsagar, G.U.Maramai, S.Chemi, G.Gemma, S.Campiani, G.Novellino, E.Fiorenzani, P.Pinassi, J.Aloisi, A.M.Gynther, M.Venskutonyte, R.Han, L.Frydenvang, K.Kastrup, J.S.Pickering, D.S.

(2018) J. Med. Chem. 61: 2124-2130

  • DOI: 10.1021/acs.jmedchem.8b00099
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Starting from 1-4 and 7 structural templates, analogues based on bioisosteric replacements (5a-c vs 1, 2 and 6 vs 7) were synthesized for completing the SAR analysis. Interesting binding properties at GluA2, GluK1 and GluK3 receptors were discovered. ...

    Starting from 1-4 and 7 structural templates, analogues based on bioisosteric replacements (5a-c vs 1, 2 and 6 vs 7) were synthesized for completing the SAR analysis. Interesting binding properties at GluA2, GluK1 and GluK3 receptors were discovered. The requirements for GluK3 interaction were elucidated determining the X-ray structures of the GluK3-LBD with 2 and 5c and by computational studies. Antinociceptive potential was demonstrated for GluK1 partial agonist 3 and antagonist 7 (2 mg/kg ip).



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
A
258Rattus norvegicusMutation(s): 0 
Gene Names: Grik3 (Glur7)
Find proteins for P42264 (Rattus norvegicus)
Go to UniProtKB:  P42264
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CGW
Query on CGW

Download SDF File 
Download CCD File 
A
(2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)-5,7-dihydrothieno[3,4-d]pyrimidin-1-yl]propanoic acid
C9 H11 N3 O4 S
PETHBUJXGHVGGK-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.040α = 90.00
b = 68.040β = 90.00
c = 126.860γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Database references
  • Version 1.2: 2018-03-21
    Type: Database references