4IGR

Crystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist ZA302


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chemoenzymatic synthesis of new 2,4-syn-functionalized (S)-glutamate analogues and structure-activity relationship studies at ionotropic glutamate receptors and excitatory amino acid transporters.

Assaf, Z.Larsen, A.P.Venskutonyte, R.Han, L.Abrahamsen, B.Nielsen, B.Gajhede, M.Kastrup, J.S.Jensen, A.A.Pickering, D.S.Frydenvang, K.Gefflaut, T.Bunch, L.

(2013) J.Med.Chem. 56: 1614-1628

  • DOI: 10.1021/jm301433m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the mammalian central nervous system, (S)-glutamate (Glu) is released from the presynaptic neuron where it activates a plethora of pre- and postsynaptic Glu receptors. The fast acting ionotropic Glu receptors (iGluRs) are ligand gated ion channels ...

    In the mammalian central nervous system, (S)-glutamate (Glu) is released from the presynaptic neuron where it activates a plethora of pre- and postsynaptic Glu receptors. The fast acting ionotropic Glu receptors (iGluRs) are ligand gated ion channels and are believed to be involved in a vast number of neurological functions such as memory and learning, synaptic plasticity, and motor function. The synthesis of 14 enantiopure 2,4-syn-Glu analogues 2b-p is accessed by a short and efficient chemoenzymatic approach starting from readily available cyclohexanone 3. Pharmacological characterization at the iGluRs and EAAT1-3 subtypes revealed analogue 2i as a selective GluK1 ligand with low nanomolar affinity. Two X-ray crystal structures of the key analogue 2i in the ligand-binding domain (LBD) of GluA2 and GluK3 were determined. Partial domain closure was seen in the GluA2-LBD complex with 2i comparable to that induced by kainate. In contrast, full domain closure was observed in the GluK3-LBD complex with 2i, similar to that of GluK3-LBD with glutamate bound.


    Related Citations: 
    • Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate.
      Venskutonyte, R.,Frydenvang, K.,Gajhede, M.,Bunch, L.,Pickering, D.S.,Kastrup, J.S.
      (2011) J.Struct.Biol. 176: 307


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
3ZA
Query on 3ZA

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Download CCD File 
A
(4R)-4-{3-[hydroxy(methyl)amino]-3-oxopropyl}-L-glutamic acid
C9 H16 N2 O6
YWTXUGAXXGHUOR-RITPCOANSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3ZAKi: 123 nM (97) BINDINGDB
3ZAKd: 63 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.198 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.180α = 90.00
b = 68.180β = 90.00
c = 126.520γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection, Refinement description, Source and taxonomy