4NWC

Crystal structure of the GluK3 ligand-binding domain (S1S2) in complex with the agonist (2S,4R)-4-(3-Methoxy-3-oxopropyl)glutamic acid at 2.01 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.012 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Recognition of Two 2,4-syn-Functionalized (S)-Glutamate Analogues by the Kainate Receptor GluK3 Ligand Binding Domain.

Venskutonyte, R.Larsen, A.P.Frydenvang, K.Gajhede, M.Sagot, E.Assaf, Z.Gefflaut, T.Pickering, D.S.Bunch, L.Kastrup, J.S.

(2014) Chemmedchem 9: 2254-2259

  • DOI: 10.1002/cmdc.201402204
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The kainate receptors are the least studied subfamily of ionotropic glutamate receptors. These receptors are thought to have a neuromodulatory role and have been associated with a variety of disorders in the central nervous system. This makes kainate ...

    The kainate receptors are the least studied subfamily of ionotropic glutamate receptors. These receptors are thought to have a neuromodulatory role and have been associated with a variety of disorders in the central nervous system. This makes kainate receptors interesting potential drug targets. Today, structures of the ligand binding domain (LBD) of the kainate receptor GluK3 are only known in complex with the endogenous agonist glutamate, the natural product kainate, and two synthetic agonists. Herein we report structures of GluK3 LBD in complex with two 2,4-syn-functionalized (S)-glutamate analogues to investigate their structural potential as chemical scaffolds. Similar binding affinities at GluK3 were determined for the 2-(methylcarbamoyl)ethyl analogue (Ki =4.0 μM) and the 2-(methoxycarbonyl)ethyl analogue (Ki =1.7 μM), in agreement with the similar positioning of the compounds within the binding pocket. As the binding affinity is similar to that of glutamate, this type of Cγ substituent could be used as a scaffold for introduction of even larger substituents reaching into unexplored binding site regions to achieve subtype selectivity.


    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 & Pharmacology, Faculty of Health & Medical Sciences, University of Copenhagen, 2100 Copenhagen (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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Download CCD File 
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
2QE
Query on 2QE

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Download CCD File 
A
(2S,4R)-4-(3-Methoxy-3-oxopropyl) glutamic acid
(4R)-4-(3-methoxy-3-oxopropyl)-L-glutamic acid
C9 H15 N O6
IPTIKQIFOOZKAT-RITPCOANSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2QEKi: 1010 nM (97) BINDINGDB
2QEKi: 1740 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.012 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.810α = 90.00
b = 67.810β = 90.00
c = 126.770γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Data collection, Refinement description, Source and taxonomy