4X48

Crystal structure of GluR2 ligand-binding core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The Discovery and Characterization of the alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Potentiator N-{(3S,4S)-4-[4-(5-Cyano-2-thienyl)phenoxy]tetrahydrofuran-3-yl}propane-2-sulfonamide (PF-04958242).

Shaffer, C.L.Patel, N.C.Schwarz, J.Scialis, R.J.Wei, Y.Hou, X.J.Xie, L.Karki, K.Bryce, D.K.Osgood, S.M.Hoffmann, W.E.Lazzaro, J.T.Chang, C.McGinnis, D.F.Lotarski, S.M.Liu, J.Obach, R.S.Weber, M.L.Chen, L.Zasadny, K.R.Seymour, P.A.Schmidt, C.J.Hajos, M.Hurst, R.S.Pandit, J.O'Donnell, C.J.

(2015) J Med Chem 58: 4291-4308

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00300
  • Primary Citation of Related Structures:  
    4X48

  • PubMed Abstract: 

    A unique tetrahydrofuran ether class of highly potent α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor potentiators has been identified using rational and structure-based drug design. An acyclic lead compound, containing an ether-linked isopropylsulfonamide and biphenyl group, was pharmacologically augmented by converting it to a conformationally constrained tetrahydrofuran to improve key interactions with the human GluA2 ligand-binding domain. Subsequent replacement of the distal phenyl motif with 2-cyanothiophene to enhance its potency, selectivity, and metabolic stability afforded N-{(3S,4S)-4-[4-(5-cyano-2-thienyl)phenoxy]tetrahydrofuran-3-yl}propane-2-sulfonamide (PF-04958242, 3), whose preclinical characterization suggests an adequate therapeutic index, aided by low projected human oral pharmacokinetic variability, for clinical studies exploring its ability to attenuate cognitive deficits in patients with schizophrenia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
A, B, C
275Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XPF
Query on XPF

Download Ideal Coordinates CCD File 
I [auth B],
M [auth C]
N-{(3S,4S)-4-[4-(5-cyanothiophen-2-yl)phenoxy]tetrahydrofuran-3-yl}propane-2-sulfonamide
C18 H20 N2 O4 S2
TTYKUKSFWHEBLI-DLBZAZTESA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
J [auth C]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth B],
K [auth C],
L [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.759α = 90
b = 164.965β = 90
c = 47.363γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTER-TNTphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2015-05-06 
  • Deposition Author(s): Pandit, J.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary