3O29

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A novel series of positive modulators of the AMPA receptor: discovery and structure based hit-to-lead studies.

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

(2010) Bioorg Med Chem Lett 20: 5753-5756

  • DOI: https://doi.org/10.1016/j.bmcl.2010.07.138
  • Primary Citation of Related Structures:  
    3O28, 3O29, 3O2A

  • PubMed Abstract: 

    Starting from an HTS derived hit 1, application of biostructural data facilitated rapid optimization to lead 22, a novel AMPA receptor modulator. This is the first demonstration of how structure based drug design can be exploited in an optimization program for a glutamate receptor.


  • Organizational Affiliation

    Merck Research Laboratories, MSD, Motherwell, Lanarkshire ML1 5SH, 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O29
Query on O29

Download Ideal Coordinates CCD File 
I [auth A]N-[2-(dimethylamino)ethyl]-2-({[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
C23 H30 F3 N5 O2 S
UXUSFGHVYPKOKQ-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]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.127α = 90
b = 88.518β = 90
c = 47.336γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: Refinement description, Source and taxonomy