3PD9

X-ray structure of the ligand-binding core of GluA2 in complex with (R)-5-HPCA at 2.1 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Biostructural and pharmacological studies of bicyclic analogues of the 3-isoxazolol glutamate receptor agonist ibotenic acid.

Frydenvang, K.Pickering, D.S.Greenwood, J.R.Krogsgaard-Larsen, N.Brehm, L.Nielsen, B.Vogensen, S.B.Hald, H.Kastrup, J.S.Krogsgaard-Larsen, P.Clausen, R.P.

(2010) J Med Chem 53: 8354-8361

  • DOI: 10.1021/jm101218a
  • Primary Citation of Related Structures:  
    3PD8, 3PD9

  • PubMed Abstract: 
  • We describe an improved synthesis and detailed pharmacological characterization of the conformationally restricted analogue of the naturally occurring nonselective glutamate receptor agonist ibotenic acid (RS)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridine-7-carboxylic acid (7-HPCA, 5) at AMPA receptor subtypes ...

    We describe an improved synthesis and detailed pharmacological characterization of the conformationally restricted analogue of the naturally occurring nonselective glutamate receptor agonist ibotenic acid (RS)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridine-7-carboxylic acid (7-HPCA, 5) at AMPA receptor subtypes. Compound 5 was shown to be a subtype-discriminating agonist at AMPA receptors with higher binding affinity and functional potency at GluA1/2 compared to GluA3/4, unlike the isomeric analogue (RS)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridine-5-carboxylic acid (5-HPCA, 4) that binds to all AMPA receptor subtypes with comparable potency. Biostructural X-ray crystallographic studies of 4 and 5 reveal different binding modes of (R)-4 and (S)-5 in the GluA2 agonist binding domain. WaterMap analysis of the GluA2 and GluA4 binding pockets with (R)-4 and (S)-5 suggests that the energy of hydration sites is ligand dependent, which may explain the observed selectivity.


    Related Citations: 
    • Three-dimensional structure of the ligand-binding core of GluR2 in complex with the agonist (S)-ATPA: implications for receptor subunit selectivity
      Lunn, M.L., Hogner, A., Stensbol, T.B., Gouaux, E., Egebjerg, J., Kastrup, J.S.
      (2003) J Med Chem 46: 872
    • Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: Crystal structures of the GluR2 ligand binding core
      Armstrong, N., Gouaux, E.
      (2000) Neuron 28: 165

    Organizational Affiliation

    Department of Medicinal Chemistry.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A, B260Rattus norvegicusMutation(s): 0 
Gene Names: Glur2Gria2RAT
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HA5 (Subject of Investigation/LOI)
Query on HA5

Download Ideal Coordinates CCD File 
C [auth A], L [auth B](5R)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridine-5-carboxylic acid
C7 H8 N2 O4
QOFAMUTZWHXYLI-SCSAIBSYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], M [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], N [auth B], O [auth B], P [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], Q [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HA5 PDBBind:  3PD9 Ki: 600 (nM) from 1 assay(s)
Binding MOAD:  3PD9 Ki: 494 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.391α = 90
b = 121.251β = 90
c = 47.547γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-09
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.4: 2018-10-10
    Changes: Data collection, Database references, Structure summary