5YBG

Crystal structure of the GluA2o LBD in complex with glutamate and LY451395


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5YBF, 5YBG

  • 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 disorders. However, AMPA-R potentiators such as LY451646 have risks of narrow bell-shaped responses in pharmacological effects, including in vivo BDNF induction ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2,Glutamate receptor 2
A, B, C, D, E, F
A, B, C, D, E, F
263Homo sapiensMutation(s): 0 
Gene Names: GRIA2GLUR2
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8SO
Query on 8SO

Download Ideal Coordinates CCD File 
AA [auth E],
H [auth A],
P [auth C]
N-[(2R)-2-[4-[4-[2-(methylsulfonylamino)ethyl]phenyl]phenyl]propyl]propane-2-sulfonamide
C21 H30 N2 O4 S2
ULRDYYKSPCRXAJ-KRWDZBQOSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
EA [auth F],
G [auth A],
M [auth B],
O [auth C],
U [auth D],
EA [auth F],
G [auth A],
M [auth B],
O [auth C],
U [auth D],
Z [auth E]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth E],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth E],
FA [auth F],
I [auth A],
L [auth A],
N [auth B],
BA [auth E],
FA [auth F],
I [auth A],
L [auth A],
N [auth B],
Q [auth C],
R [auth C],
V [auth D],
W [auth D],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth E],
J [auth A],
S [auth C],
T [auth C],
X [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8SO Binding MOAD:  5YBG IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.724α = 90
b = 161.913β = 89.97
c = 46.964γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata 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: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references