4GXS

Ligand binding domain of GluA2 (AMPA/glutamate receptor) bound to (-)-kaitocephalin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9634 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of (-)-kaitocephalin bound to the ligand binding domain of the (S)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/glutamate receptor, GluA2.

Ahmed, A.H.Hamada, M.Shinada, T.Ohfune, Y.Weerasinghe, L.Garner, P.P.Oswald, R.E.

(2012) J.Biol.Chem. 287: 41007-41013

  • DOI: 10.1074/jbc.M112.416362

  • PubMed Abstract: 
  • Glutamate receptors mediate the majority of excitatory synaptic transmission in the central nervous system, and excessive stimulation of these receptors is involved in a variety of neurological disorders and neuronal damage from stroke. The developme ...

    Glutamate receptors mediate the majority of excitatory synaptic transmission in the central nervous system, and excessive stimulation of these receptors is involved in a variety of neurological disorders and neuronal damage from stroke. The development of new subtype-specific antagonists would be of considerable therapeutic interest. Natural products can provide important new lead compounds for drug discovery. The only natural product known to inhibit glutamate receptors competitively is (-)-kaitocephalin, which was isolated from the fungus Eupenicillium shearii and found to protect CNS neurons from excitotoxicity. Previous work has shown that it is a potent antagonist of some subtypes of glutamate receptors (AMPA and NMDA, but not kainate). The structure of kaitocephalin bound to the ligand binding domain of the AMPA receptor subtype, GluA2, is reported here. The structure suggests how kaitocephalin can be used as a scaffold to develop more selective and high affinity antagonists for glutamate receptors.


    Organizational Affiliation

    Department of Molecular Medicine, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
B, D
258Rattus norvegicusMutation(s): 0 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
0YS
Query on 0YS

Download SDF File 
Download CCD File 
B, D
(5R)-2-[(1S,2R)-2-amino-2-carboxy-1-hydroxyethyl]-5-{(2S)-2-carboxy-2-[(3,5-dichloro-4-hydroxybenzoyl)amino]ethyl}-L-proline
(-)-kaitocephalin
C18 H21 Cl2 N3 O9
AJQRDRIPQOAJCM-BWOKQULHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0YSIC50: 100000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9634 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.741α = 90.00
b = 121.466β = 90.00
c = 48.899γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXmodel building
HKL-3000data scaling
HKL-3000data collection
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-07
    Type: Database references
  • Version 1.2: 2013-06-19
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Source and taxonomy