5YBF

Crystal structure of the GluA2o LBD in complex with glutamate and HBT1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

HBT1, a Novel AMPA Receptor Potentiator with Lower Agonistic Effect, Avoided Bell-Shaped Response in In Vitro BDNF Production.

Kunugi, A.Tajima, Y.Kuno, H.Sogabe, S.Kimura, H.

(2018) J Pharmacol Exp Ther 364: 377-389

  • DOI: 10.1124/jpet.117.245050
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • α -Amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor (AMPA-R) potentiators with brain-derived neurotrophic factor (BDNF)-induction potential could be promising as therapeutic drugs for neuropsychiatric and neurologic disorde ...

    α -Amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor (AMPA-R) potentiators with brain-derived neurotrophic factor (BDNF)-induction potential could be promising as therapeutic drugs for neuropsychiatric and neurologic disorders. However, AMPA-R potentiators such as LY451646 have risks of narrow bell-shaped responses in pharmacological effects, including in vivo BDNF induction. Interestingly, LY451646 and LY451395, other AMPA-R potentiators, showed agonistic effects and exhibited bell-shaped responses in the BDNF production in primary neurons. We hypothesized that the agonistic property is related to the bell-shaped response and endeavored to discover novel AMPA-R potentiators with lower agonistic effects. LY451395 showed an agonistic effect in primary neurons, but not in a cell line expressing AMPA-Rs, in Ca 2+ influx assays; thus, we used a Ca 2+ influx assay in primary neurons and, from a chemical library, discovered two AMPA-R potentiators with lower agonistic effects: 2-(((5-methyl-3-(trifluoromethyl)-1H-pyrazol-1-yl)acetyl)amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide (HBT1) and (3S)-1-(4-tert-butylphenyl)-N-((1R)-2-(dimethylamino)-1-phenylethyl)-3-isobutyl-2-oxopyrrolidine-3-carboxamide (OXP1). In a patch-clamp study using primary neurons, HBT1 showed little agonistic effect, whereas both LY451395 and OXP1 showed remarkable agonistic effects. HBT1, but not OXP1, did not show remarkable bell-shaped response in BDNF production in primary neurons. HBT1 bound to the ligand-binding domain (LBD) of AMPA-R in a glutamate-dependent manner. The mode of HBT1 and LY451395 binding to a pocket in the LBD of AMPA-R differed: HBT1, but not LY451395, formed hydrogen bonds with S518 in the LBD. OXP1 may bind to a cryptic binding pocket on AMPA-R. Lower agonistic profile of HBT1 may associate with its lower risks of bell-shaped responses in BDNF production in primary neurons.


    Organizational Affiliation

    Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan haruhide.kimura@takeda.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2,Glutamate receptor 2
A, B, C, D, E, F
263Homo sapiensMutation(s): 0 
Gene Names: GRIA2GLUR2
Find proteins for P42262 (Homo sapiens)
Go to UniProtKB:  P42262
NIH Common Fund Data Resources
PHAROS  P42262
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8SR
Query on 8SR

Download CCD File 
A, C, E
2-[2-[5-methyl-3-(trifluoromethyl)pyrazol-1-yl]ethanoylamino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
C16 H17 F3 N4 O2 S
PHLXSNIEQIKENK-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 
A, B, C, D, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8SRKd:  543   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.596α = 90
b = 162.074β = 89.99
c = 47.103γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references