5ZG0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


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:  
    5ZG3, 5ZG2, 5ZG1, 5ZG0

  • 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A, B, C, D, E, F263Homo sapiensMutation(s): 0 
Gene Names: GLUR2GRIA2
UniProt & NIH Common Fund Data Resources
Find proteins for P42262 (Homo sapiens)
Explore P42262 
Go to UniProtKB:  P42262
PHAROS:  P42262
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9C3 (Subject of Investigation/LOI)
Query on 9C3

Download Ideal Coordinates CCD File 
I [auth B], M [auth C], Y [auth E]9-{4-[(propan-2-yl)oxy]phenyl}-3,4-dihydro-2H-2lambda~6~-pyrido[2,1-c][1,2,4]thiadiazine-2,2-dione
C16 H18 N2 O3 S
FNMSASHKBXSERE-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
CA [auth F], G [auth A], J [auth B], N [auth C], R [auth D], Z [auth E]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E] , BA [auth E] , DA [auth F] , EA [auth F] , FA [auth F] , H [auth A] , K [auth B] , L [auth B] , 
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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-2000data reduction
cctbx.primedata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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