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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1016/j.bmcl.2011.06.088
  • Primary Citation of Related Structures:  
    3S9S

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma284Homo sapiensMutation(s): 0 
Gene Names: NR1C3, PPARG
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 113Homo sapiensMutation(s): 0 
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M0T
Query on M0T
Download Ideal Coordinates CCD File 
C [auth A]1-(3,4-dichlorobenzyl)-2-methyl-N-[(1R)-1-phenylpropyl]-1H-benzimidazole-5-carboxamide
C25 H23 Cl2 N3 O
LDYDIGPGIRJQAU-JOCHJYFZSA-N
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description