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 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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: NR1C3PPARG
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B
13Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0T
Query on M0T

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 
  • R-Value Observed: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.086α = 90
b = 88.754β = 90
c = 122.605γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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