3S2V

Crystal Structure of the Ligand Binding Domain of GluK1 in Complex with an Antagonist (S)-1-(2'-Amino-2'-carboxyethyl)-3-[(2-carboxythien-3-yl)methyl]thieno[3,4-d]pyrimidin-2,4-dione at 2.5 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Selective kainate receptor (GluK1) ligands structurally based upon 1H-cyclopentapyrimidin-2,4(1H,3H)-dione: synthesis, molecular modeling, and pharmacological and biostructural characterization.

Venskutonyte, R.Butini, S.Coccone, S.S.Gemma, S.Brindisi, M.Kumar, V.Guarino, E.Maramai, S.Valenti, S.Amir, A.Valades, E.A.Frydenvang, K.Kastrup, J.S.Novellino, E.Campiani, G.Pickering, D.S.

(2011) J.Med.Chem. 54: 4793-4805

  • DOI: 10.1021/jm2004078

  • PubMed Abstract: 
  • The physiological function of kainate receptors (GluK1-GluK5) in the central nervous system is not fully understood yet. With the aim of developing potent and selective GluK1 ligands, we have synthesized a series of new thiophene-based GluK1 agonists ...

    The physiological function of kainate receptors (GluK1-GluK5) in the central nervous system is not fully understood yet. With the aim of developing potent and selective GluK1 ligands, we have synthesized a series of new thiophene-based GluK1 agonists (6a-c) and antagonists (7a-d). Pharmacological evaluation revealed that they are selective for the GluK1 subunit, with 7b being the most subtype-selective ligand reported to date (GluK1 vs GluK3). The antagonist 7a was cocrystallized with the GluK1 ligand binding domain, and an X-ray crystallographic analysis revealed the largest flexibility in GluK1 ligand binding domain opening upon binding of a ligand seen to date. The results provide new insights into the molecular mechanism of GluK1 receptor ligand binding and pave the way to the development of new tool compounds for studying kainate receptor function.


    Related Citations: 
    • Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate.
      Naur, P.,Vestergaard, B.,Skov, L.K.,Egebjerg, J.,Gajhede, M.,Kastrup, J.S.
      (2005) Febs Lett. 579: 1154


    Organizational Affiliation

    Department of Pharmacology and Pharmacotherapy, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor, ionotropic kainate 1
A, B
257Rattus norvegicusMutation(s): 0 
Gene Names: Grik1 (Glur5)
Find proteins for P22756 (Rattus norvegicus)
Go to UniProtKB:  P22756
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3HU
Query on 3HU

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Download CCD File 
A, B
(S)-1-(2'-AMINO-2'-CARBOXYETHYL)-3-[(2-CARBOXYTHIEN-3-YL)METHYL]THIENO[3,4-D]PYRIMIDIN-2,4-DIONE
C15 H13 N3 O6 S2
LSNSPQPOGKSTHQ-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3HUKi: 98950 nM (88) BINDINGDB
3HUKi: 157 nM BINDINGMOAD
3HUKi: 157 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.459α = 90.00
b = 93.353β = 90.00
c = 107.171γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-23
    Type: Database references
  • Version 1.3: 2017-08-09
    Type: Data collection, Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-08
    Type: Refinement description