5ZG2

Crystal structure of the GluA2o LBD in complex with ZK200775 and Compound-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B
263Homo sapiensMutation(s): 0 
Gene Names: GLUR2
UniProt & NIH Common Fund Data Resources
Find proteins for P42262 (Homo sapiens)
Go to UniProtKB:  P42262
PHAROS:  P42262
GTEx:  ENSG00000120251 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZK1
Query on ZK1

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
C14 H15 F3 N3 O6 P
WZMQMKNCWDCCMT-UHFFFAOYSA-N
9C0
Query on 9C0

Download Ideal Coordinates CCD File 
D [auth A]9-(4-~{tert}-butylphenyl)-3,4-dihydropyrido[2,1-c][1,2,4]thiadiazine 2,2-dioxide
C17 H20 N2 O2 S
NFUZLMGYOAJDAK-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B],
N [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.384α = 90
b = 56.565β = 91.74
c = 90.779γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

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