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 

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Ligand Structure Quality Assessment 


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
  • 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C, D, E, F
A, B, C, D, E, F
263Homo sapiensMutation(s): 0 
Gene Names: GLUR2
UniProt & NIH Common Fund Data Resources
Find proteins for P42262 (Homo sapiens)
Explore P42262 
Go to UniProtKB:  P42262
PHAROS:  P42262
GTEx:  ENSG00000120251 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42262
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9C6
Query on 9C6
Download Ideal Coordinates CCD File 
BA [auth E],
G [auth A],
U [auth D]		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 Ideal Coordinates CCD File 
CA [auth E],
GA [auth F],
H [auth A],
I [auth B],
O [auth C],
CA [auth E],
GA [auth F],
H [auth A],
I [auth B],
O [auth C],
V [auth D]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AA [auth D],
DA [auth E],
FA [auth F],
HA [auth F],
IA [auth F],
AA [auth D],
DA [auth E],
FA [auth F],
HA [auth F],
IA [auth F],
J [auth B],
M [auth B],
N [auth C],
P [auth C],
T [auth D],
W [auth D],
X [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
EA [auth E],
JA [auth F],
K [auth B],
KA [auth F],
L [auth B],
EA [auth E],
JA [auth F],
K [auth B],
KA [auth F],
L [auth B],
LA [auth F],
Q [auth C],
R [auth C],
S [auth C],
Y [auth D],
Z [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9C6 Binding MOAD:  5ZG3 Ki: 61 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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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