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

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jm301590z
  • Primary Citation of Related Structures:  

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2A,
B [auth D],
D [auth B]
263Rattus norvegicusMutation(s): 0 
Gene Names: Glur2Gria2
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
I [auth D]
L [auth C]
M [auth C]
Q [auth B]
F [auth A],
I [auth D],
L [auth C],
M [auth C],
Q [auth B],
R [auth B]
O4 S
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth D]
K [auth D]
N [auth C]
G [auth A],
H [auth A],
J [auth D],
K [auth D],
N [auth C],
O [auth C],
S [auth B],
T [auth B]
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

  • 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
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description