4ISU

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the antagonist (2R)-IKM-159 at 2.3A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Studies on an (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) receptor antagonist IKM-159: asymmetric synthesis, neuroactivity, and structural characterization.

Juknaite, L.Sugamata, Y.Tokiwa, K.Ishikawa, Y.Takamizawa, S.Eng, A.Sakai, R.Pickering, D.S.Frydenvang, K.Swanson, G.T.Kastrup, J.S.Oikawa, M.

(2013) J Med Chem 56: 2283-2293

  • DOI: 10.1021/jm301590z
  • Primary Citation of Related Structures:  
    4ISU

  • PubMed Abstract: 
  • IKM-159 was developed and identified as a member of a new class of heterotricyclic glutamate analogues that act as AMPA receptor-selective antagonists. However, it was not known which enantiomer of IKM-159 was responsible for its pharmacological activities ...

    IKM-159 was developed and identified as a member of a new class of heterotricyclic glutamate analogues that act as AMPA receptor-selective antagonists. However, it was not known which enantiomer of IKM-159 was responsible for its pharmacological activities. Here, we report in vivo and in vitro neuronal activities of both enantiomers of IKM-159 prepared by enantioselective asymmetric synthesis. By employment of (R)-2-amino-2-(4-methoxyphenyl)ethanol as a chiral auxiliary, (2R)-IKM-159 and the (2S)-counterpart were successfully synthesized in 0.70% and 1.5% yields, respectively, over a total of 18 steps. Both behavioral and electrophysiological assays showed that the biological activity observed for the racemic mixture was reproduced only with (2R)-IKM-159, whereas the (2S)-counterpart was inactive in both assays. Racemic IKM-159 was crystallized with the ligand-binding domain of GluA2, and the structure revealed a complex containing (2R)-IKM-159 at the glutamate binding site. (2R)-IKM-159 locks the GluA2 in an open form, consistent with a pharmacological action as competitive antagonist of AMPA receptors.


    Organizational Affiliation

    Graduate School of Nanobioscience, Yokohama City University , Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A, D [auth B], C, B [auth D]263Rattus norvegicusMutation(s): 0 
Gene Names: Glur2Gria2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IKM (Subject of Investigation/LOI)
Query on IKM

Download Ideal Coordinates CCD File 
E [auth A], P [auth B](4aS,5aR,6R,8aS,8bS)-5a-(carboxymethyl)-8-oxo-2,4a,5a,6,7,8,8a,8b-octahydro-1H-pyrrolo[3',4':4,5]furo[3,2-b]pyridine-6-carboxylic acid
C12 H14 N2 O6
RVLCVCHOUKAPIG-WCPLEAOBSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], I [auth D], L [auth C], M [auth C], Q [auth B], R [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], J [auth D], K [auth D], N [auth C], O [auth C], S [auth B], T [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IKM Binding MOAD:  4ISU Ki: 2.10e+5 (nM) from 1 assay(s)
PDBBind:  4ISU Ki: 2.10e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.514α = 90
b = 88.773β = 90
c = 194.456γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Data collection, Refinement description, Source and taxonomy