3O6H

Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted O25Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

A novel series of positive modulators of the AMPA receptor: structure-based lead optimization.

Jamieson, C.Campbell, R.A.Cumming, I.A.Gillen, K.J.Gillespie, J.Kazemier, B.Kiczun, M.Lamont, Y.Lyons, A.J.Maclean, J.K.Martin, F.Moir, E.M.Morrow, J.A.Pantling, J.Rankovic, Z.Smith, L.

(2010) Bioorg Med Chem Lett 20: 6072-6075

  • DOI: https://doi.org/10.1016/j.bmcl.2010.08.063
  • Primary Citation of Related Structures:  
    3O6G, 3O6H, 3O6I

  • PubMed Abstract: 

    Starting from lead compound 1, we demonstrate how X-ray structural data can be used to understand SAR and expediently optimize bioavailability in a novel series of AMPA receptor modulators, furnishing 5 with improved bioavailability and robust in vivo activity.


  • Organizational Affiliation

    Merck Research Laboratories, MSD, Newhouse, Motherwell, Lanarkshire, UK. craig.jamieson@strath.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2263Rattus 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O25
Query on O25

Download Ideal Coordinates CCD File 
F [auth A]2-[({4-[(ethylamino)methyl]-3-(trifluoromethyl)-1H-pyrazol-1-yl}acetyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
C18 H22 F3 N5 O2 S
MEANENDBNRVQSP-UHFFFAOYSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
B [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.89α = 90
b = 87.45β = 90
c = 47.32γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted O25Click on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-09
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.3: 2024-11-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary