6F28

Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2'-Amino-2'-carboxyethyl]-6-methyl-5,7-dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.4A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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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: https://doi.org/10.1021/acs.jmedchem.8b00099
  • Primary Citation of Related Structures:  
    6F28, 6F29

  • 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. The requirements for GluK3 interaction were elucidated by determining the X-ray structures of the GluK3-LBD with 2 and 5c and by computational studies ...

    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 by 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).

    Organizational Affiliation: 

    Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , DK-2100 Copenhagen , Denmark.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
A, B
258Rattus norvegicusMutation(s): 0 
Gene Names: Grik3, Glur7
UniProt
Find proteins for P42264 (Rattus norvegicus)
Explore P42264 
Go to UniProtKB:  P42264
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42264
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
CG8 Binding MOAD:  6F28 Ki: 2150 (nM) from 1 assay(s)
BindingDB:  6F28 Ki: 2150 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.039α = 90
b = 56.214β = 90
c = 87.189γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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