3PMX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure based evolution of a novel series of positive modulators of the AMPA receptor.

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

(2011) Bioorg Med Chem Lett 21: 805-811

  • DOI: 10.1016/j.bmcl.2010.11.098
  • Primary Citation of Related Structures:  
    3PMX, 3PMV, 3PMW

  • PubMed Abstract: 
  • Starting from compound 1, we utilized biostructural data to successfully evolve an existing series into a new chemotype with a promising overall profile, exemplified by 19.


    Organizational Affiliation

    Merck Research Laboratories, MSD, Newhouse, Motherwell, Lanarkshire ML1 5SH, UK. craig.jamieson@strath.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
808
Query on 808

Download Ideal Coordinates CCD File 
A
N-[(2S)-5-{[5-(trifluoromethyl)furan-2-yl]methyl}-2,3-dihydro-1H-inden-2-yl]propane-2-sulfonamide
C18 H20 F3 N O3 S
LONAEEDHLGMMRS-HNNXBMFYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
808EC50:  1000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.24α = 90
b = 88.17β = 90
c = 47.345γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    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