4YMA

Structure of the ligand-binding domain of GluA2 in complex with the antagonist CNG10109


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.895 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-Activity Relationship Study of Ionotropic Glutamate Receptor Antagonist (2S,3R)-3-(3-Carboxyphenyl)pyrrolidine-2-carboxylic Acid.

Krogsgaard-Larsen, N.Storgaard, M.Moller, C.Demmer, C.S.Hansen, J.Han, L.Monrad, R.N.Nielsen, B.Tapken, D.Pickering, D.S.Kastrup, J.S.Frydenvang, K.Bunch, L.

(2015) J.Med.Chem. 58: 6131-6150

  • DOI: 10.1021/acs.jmedchem.5b00750
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herein we describe the first structure-activity relationship study of the broad-range iGluR antagonist (2S,3R)-3-(3-carboxyphenyl)pyrrolidine-2-carboxylic acid (1) by exploring the pharmacological effect of substituents in the 4, 4', or 5' positions ...

    Herein we describe the first structure-activity relationship study of the broad-range iGluR antagonist (2S,3R)-3-(3-carboxyphenyl)pyrrolidine-2-carboxylic acid (1) by exploring the pharmacological effect of substituents in the 4, 4', or 5' positions and the bioisosteric substitution of the distal carboxylic acid for a phosphonic acid moiety. Of particular interest is a hydroxyl group in the 4' position 2a which induced a preference in binding affinity for homomeric GluK3 over GluK1 (Ki = 0.87 and 4.8 μM, respectively). Two X-ray structures of ligand binding domains were obtained: 2e in GluA2-LBD and 2f in GluK1-LBD, both at 1.9 Å resolution. Compound 2e induces a D1-D2 domain opening in GluA2-LBD of 17.3-18.8° and 2f a domain opening in GluK1-LBD of 17.0-17.5° relative to the structures with glutamate. The pyrrolidine-2-carboxylate moiety of 2e and 2f shows a similar binding mode as kainate. The 3-carboxyphenyl ring of 2e and 2f forms contacts comparable to those of the distal carboxylate in kainate.


    Related Citations: 
    • L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain.
      Krintel, C.,Frydenvang, K.,Ceravalls de Rabassa, A.,Kaern, A.M.,Gajhede, M.,Pickering, D.S.,Kastrup, J.S.
      (2014) FEBS J. 281: 2422


    Organizational Affiliation

    †Chemical Neuroscience Group, ‡Biostructural Research Group, §Medicinal Chemistry Group, ∥Molecular, Cellular Pharmacology Group, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
B, A
264Rattus norvegicusMutation(s): 0 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 5 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
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
4E5
Query on 4E5

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Download CCD File 
A, B
(3R)-3-(3-carboxy-5-hydroxyphenyl)-L-proline
C12 H13 N O5
RMJSXKKIOKMPOU-ZJUUUORDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.895 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.880α = 90.00
b = 65.250β = 92.36
c = 91.550γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Denmark--

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Data collection, Database references
  • Version 1.3: 2018-03-07
    Type: Source and taxonomy