3S9S

Ligand binding domain of PPARgamma complexed with a benzimidazole partial agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of GSK1997132B a novel centrally penetrant benzimidazole PPARgamma partial agonist.

Sime, M.Allan, A.C.Chapman, P.Fieldhouse, C.Giblin, G.M.Healy, M.P.Lambert, M.H.Leesnitzer, L.M.Lewis, A.Merrihew, R.V.Rutter, R.A.Sasse, R.Shearer, B.G.Wilson, T.M.Xu, R.X.Virley, D.J.

(2011) Bioorg.Med.Chem.Lett. 21: 5568-5572

  • DOI: 10.1016/j.bmcl.2011.06.088

  • PubMed Abstract: 
  • The peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated nuclear receptor, thought to play a role in energy metabolism, glucose homeostasis and microglia-mediated neuroinflammation. A novel benzimidazole series of centrally pene ...

    The peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated nuclear receptor, thought to play a role in energy metabolism, glucose homeostasis and microglia-mediated neuroinflammation. A novel benzimidazole series of centrally penetrant PPARγ partial agonists has been identified. The optimization of PPARγ activity and in vivo pharmacokinetics leading to the identification of GSK1997132B a potent, metabolically stable and centrally penetrant PPARγ partial agonist, is described.


    Organizational Affiliation

    Neurosciences Centre for Excellence in Drug Discovery, GlaxoSmithKline, New Frontiers Science Park, Harlow, Essex, CM19 5AW, United Kingdom. m.sime@beatson.gla.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
284Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B
13Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0T
Query on M0T

Download SDF File 
Download CCD File 
A
1-(3,4-dichlorobenzyl)-2-methyl-N-[(1R)-1-phenylpropyl]-1H-benzimidazole-5-carboxamide
C25 H23 Cl2 N3 O
LDYDIGPGIRJQAU-JOCHJYFZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 56.086α = 90.00
b = 88.754β = 90.00
c = 122.605γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
ADSCdata collection
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release