5CC2

STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE IONOTROPIC GLUTAMATE RECEPTOR-LIKE GLUD2 IN COMPLEX WITH 7-CKA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pharmacology and Structural Analysis of Ligand Binding to the Orthosteric Site of Glutamate-Like GluD2 Receptors.

Kristensen, A.S.Hansen, K.B.Naur, P.Olsen, L.Kurtkaya, N.L.Dravid, S.M.Kvist, T.Yi, F.Phlsgaard, J.Clausen, R.P.Gajhede, M.Kastrup, J.S.Traynelis, S.F.

(2016) Mol.Pharmacol. 89: 253-262

  • DOI: 10.1124/mol.115.100909

  • PubMed Abstract: 
  • The GluD2 receptor is a fundamental component of postsynaptic sites in Purkinje neurons, and is required for normal cerebellar function. GluD2 and the closely related GluD1 are classified as members of the ionotropic glutamate receptor (iGluR) superf ...

    The GluD2 receptor is a fundamental component of postsynaptic sites in Purkinje neurons, and is required for normal cerebellar function. GluD2 and the closely related GluD1 are classified as members of the ionotropic glutamate receptor (iGluR) superfamily on the basis of sequence similarity, but do not bind l-glutamate. The amino acid neurotransmitter D-Ser is a GluD2 receptor ligand, and endogenous D-Ser signaling through GluD2 has recently been shown to regulate endocytosis of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-type iGluRs during synaptic plasticity in the cerebellum, such as long-term depression. Here, we investigate the pharmacology of the orthosteric binding site in GluD2 by examining the activity of analogs of D-Ser and GluN1 glycine site competitive antagonists at GluD2 receptors containing the lurcher mutation (GluD2(LC)), which promotes spontaneous channel activation. We identify several compounds that modulate GluD2(LC), including a halogenated alanine analog as well as the kynurenic acid analog 7-chloro-4-oxo-1H-quinoline-2-carboxylic acid (7-chlorokynurenic acid; 7-CKA). By correlating thermodynamic and structural data for 7-CKA binding to the isolated GluD2 ligand binding domain (GluD2-LBD), we find that binding 7-CKA to GluD2-LBD differs from D-Ser by inducing an intermediate cleft closure of the clamshell-shaped LBD. The GluD2 ligands identified here can potentially serve as a starting point for development of GluD2-selective ligands useful as tools in studies of the signaling role of the GluD2 receptor in the brain.


    Related Citations: 
    • Ionotropic glutamate-like receptor delta2 binds D-serine and glycine.
      Naur, P.,Hansen, K.B.,Kristensen, A.S.,Dravid, S.M.,Pickering, D.S.,Olsen, L.,Vestergaard, B.,Egebjerg, J.,Gajhede, M.,Traynelis, S.F.,Kastrup, J.S.
      (2007) Proc. Natl. Acad. Sci. U.S.A. 104: 14116


    Organizational Affiliation

    Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (A.S.K., K.B.H., N.L.K., S.M.D., S.F.T.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.S.K., P.N., L.O., T.K., J.P., R.P.C., M.G., J.S.K.); and Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (K.B.H., F.Y.).,Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia (A.S.K., K.B.H., N.L.K., S.M.D., S.F.T.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.S.K., P.N., L.O., T.K., J.P., R.P.C., M.G., J.S.K.); and Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (K.B.H., F.Y.) strayne@emory.edu jsk@sund.ku.dk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, delta-2
A
265Rattus norvegicusMutation(s): 0 
Gene Names: Grid2
Find proteins for Q63226 (Rattus norvegicus)
Go to UniProtKB:  Q63226
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CKA
Query on CKA

Download SDF File 
Download CCD File 
A
7-Chlorokynurenic acid
7-CKA
C10 H6 Cl N O3
UAWVRVFHMOSAPU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CKAKd: 80000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.210α = 90.00
b = 70.210β = 90.00
c = 134.500γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
Cootmodel building
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection