2XX8

Crystal structure of N,N-dimethyl-4-(3-(trifluoromethyl)-4,5,6,7- tetrahydro-1H-indazol-1-yl)benzamide in complex with the ligand binding domain of the Rat GluA2 receptor and glutamate at 2.2A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Integration of Lead Optimization with Crystallography for a Membrane-Bound Ion Channel Target: Discovery of a New Class of Ampa Receptor Positive Allosteric Modulators.

Ward, S.E.Harries, M.Aldegheri, L.Austin, N.E.Ballantine, S.Ballini, E.Bradley, D.M.Bax, B.D.Clarke, B.P.Harris, A.J.Harrison, S.A.Melarange, R.A.Mookherjee, C.Mosley, J.Dal Negro, G.Oliosi, B.Smith, K.J.Thewlis, K.M.Woollard, P.M.Yusaf, S.P.

(2011) J.Med.Chem. 54: 78

  • DOI: 10.1021/jm100679e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A novel series of AMPAR positive modulators is described that were identified by high throughput screening. The molecules of the series have been optimized from a high quality starting point hit to afford excellent developability, tolerability, and e ...

    A novel series of AMPAR positive modulators is described that were identified by high throughput screening. The molecules of the series have been optimized from a high quality starting point hit to afford excellent developability, tolerability, and efficacy profiles, leading to identification of a clinical candidate. Unusually for an ion channel target, this optimization was integrated with regular generation of ligand-bound crystal structures and uncovered a novel chemotype with a unique and highly conserved mode of interaction via a trifluoromethyl group.


    Organizational Affiliation

    School of Life Sciences, University of Sussex, Brighton, United Kingdom. simon.ward@sussex.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RECEPTOR 2
A, B, C
263Rattus norvegicusMutation(s): 1 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 4 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
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
1NE
Query on 1NE

Download SDF File 
Download CCD File 
A, B
N,N-DIMETHYL-4-[3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-INDAZOL-1-YL]BENZAMIDE
C17 H18 F3 N3 O
UDKLBQULCJTEOC-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.939α = 90.00
b = 163.663β = 90.00
c = 47.379γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-09-28
    Type: Database references, Version format compliance