Crystal structure of the GluA2o LBD in complex with glutamate and Compound-1

Experimental Data Snapshot

  • Resolution: 1.58 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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TAK-137, an AMPA-R potentiator with little agonistic effect, has a wide therapeutic window.

Kunugi, A.Tanaka, M.Suzuki, A.Tajima, Y.Suzuki, N.Suzuki, M.Nakamura, S.Kuno, H.Yokota, A.Sogabe, S.Kosugi, Y.Awasaki, Y.Kaku, T.Kimura, H.

(2019) Neuropsychopharmacology 44: 961-970

  • DOI: https://doi.org/10.1038/s41386-018-0213-7
  • Primary Citation of Related Structures:  
    5ZG0, 5ZG1, 5ZG2, 5ZG3

  • PubMed Abstract: 

    Activation of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor (AMPA-R) is a promising strategy to treat psychiatric and neurological diseases if issues of bell-shaped response and narrow safety margin against seizure can be overcome. Here, we show that structural interference at Ser743 in AMPA-R is a key to lower the agonistic effect of AMPA-R potentiators containing dihydropyridothiadiazine 2,2-dioxides skeleton. With this structural insight, TAK-137, 9-(4-phenoxyphenyl)-3,4-dihydropyrido[2,1-c][1,2,4]thiadiazine 2,2-dioxide, was discovered as a novel AMPA-R potentiator with a lower agonistic effect than an AMPA-R potentiator LY451646 ((R)-N-(2-(4'-cyanobiphenyl-4-yl)propyl)propane-2-sulfonamide) in rat primary neurons. TAK-137 induced brain-derived neurotrophic factor in neurons in rodents and potently improved cognition in both rats and monkeys. Compared to LY451646, TAK-137 had a wider safety margin against seizure in rats. TAK-137 enhanced neural progenitor proliferation over a broader range of doses in rodents. Thus, TAK-137 is a promising AMPA-R potentiator with potent procognitive effects and lower risks of bell-shaped response and seizure. These data may open the door for the development of AMPA-R potentiators as therapeutic drugs for psychiatric and neurological diseases.

  • Organizational Affiliation

    Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C, D, E
A, B, C, D, E, F
263Homo sapiensMutation(s): 0 
Gene Names: GLUR2GRIA2
UniProt & NIH Common Fund Data Resources
Find proteins for P42262 (Homo sapiens)
Explore P42262 
Go to UniProtKB:  P42262
GTEx:  ENSG00000120251 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42262
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9C3

Download Ideal Coordinates CCD File 
I [auth B],
M [auth C],
Y [auth E]
C16 H18 N2 O3 S
Query on GLU

Download Ideal Coordinates CCD File 
CA [auth F]
G [auth A]
J [auth B]
N [auth C]
R [auth D]
CA [auth F],
G [auth A],
J [auth B],
N [auth C],
R [auth D],
Z [auth E]
C5 H9 N O4
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
DA [auth F]
EA [auth F]
FA [auth F]
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
FA [auth F],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
S [auth D],
T [auth D],
U [auth D]
Query on ACT

Download Ideal Coordinates CCD File 
GA [auth F]
HA [auth F]
P [auth C]
Q [auth C]
V [auth D]
GA [auth F],
HA [auth F],
P [auth C],
Q [auth C],
V [auth D],
W [auth D],
X [auth D]
C2 H3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
9C3 Binding MOAD:  5ZG0 Ki: 82 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.58 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.682α = 90
b = 162.582β = 90
c = 47.383γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
cctbx.primedata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description