4LZ8

Crystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery and Characterization of a Novel Dihydroisoxazole Class of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) Receptor Potentiators.

Patel, N.C.Schwarz, J.Hou, X.J.Hoover, D.J.Xie, L.Fliri, A.J.Gallaschun, R.J.Lazzaro, J.T.Bryce, D.K.Hoffmann, W.E.Hanks, A.N.McGinnis, D.Marr, E.S.Gazard, J.L.Hajos, M.Scialis, R.J.Hurst, R.S.Shaffer, C.L.Pandit, J.O'Donnell, C.J.

(2013) J.Med.Chem. 56: 9180-9191

  • DOI: 10.1021/jm401274b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Positive allosteric modulators ("potentiators") of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (AMPAR) enhance excitatory neurotransmission and may improve the cognitive deficits associated with various neurological disorder ...

    Positive allosteric modulators ("potentiators") of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (AMPAR) enhance excitatory neurotransmission and may improve the cognitive deficits associated with various neurological disorders. The dihydroisoxazole (DHI) series of AMPAR potentiators described herein originated from the identification of 7 by a high-throughput functional activity screen using mouse embryonic stem (mES) cell-derived neuronal precursors. Subsequent structure-based drug design using X-ray crystal structures of the ligand-binding domain of human GluA2 led to the discovery of both PF-04725379 (11), which in tritiated form became a novel ligand for characterizing the binding affinities of subsequent AMPAR potentiators in rat brain homogenate, and PF-04701475 (8a), a prototype used to explore AMPAR-mediated pharmacology in vivo. Lead series optimization provided 16a, a functionally potent compound lacking the potentially bioactivatable aniline within 8a, but retaining desirable in vitro ADME properties.


    Organizational Affiliation

    Pfizer Worldwide Research and Development, Groton Laboratories , 445 Eastern Point Road, Groton, Connecticut 06340, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A, B, C
275Rattus norvegicusMutation(s): 3 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
A, B, C
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
1YX
Query on 1YX

Download SDF File 
Download CCD File 
A, B
N-[(3S)-1-{2-fluoro-4-[(5S)-5-{[(propan-2-ylsulfonyl)amino]methyl}-4,5-dihydro-1,2-oxazol-3-yl]phenyl}pyrrolidin-3-yl]acetamide
C19 H27 F N4 O4 S
XCANXEILGPMNGT-HOTGVXAUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.676α = 90.00
b = 164.953β = 90.00
c = 47.498γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-31 
  • Released Date: 2013-12-04 
  • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy