5ZG3

Crystal structure of the GluA2o LBD in complex with glutamate and TAK-137

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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: 10.1038/s41386-018-0213-7
  • Structures With Same Primary Citation

  • 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. H ...

    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. haruhide.kimura@takeda.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B, C, D, E, F
263Homo sapiensMutation(s): 0 
Gene Names: GLUR2
Find proteins for P42262 (Homo sapiens)
Go to UniProtKB:  P42262
NIH Common Fund Data Resources
PHAROS  P42262
GTEx  ENSG00000120251
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9C6
Query on 9C6
Download CCD File 
A, D, E
9-(4-phenoxyphenyl)-3,4-dihydro-2H-2lambda~6~-pyrido[2,1-c][1,2,4]thiadiazine-2,2-dione
C19 H16 N2 O3 S
VKKLOYOLCCDGLD-UHFFFAOYSA-N		 Ligand Interaction
GLU
Query on GLU
Download CCD File 
A, B, C, D, E, F
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download CCD File 
B, C, D, E, F
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.065α = 90
b = 162.332β = 90.02
c = 47.385γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references