3S9S

Ligand binding domain of PPARgamma complexed with a benzimidazole partial agonist

• PDB DOI:  https://doi.org/10.2210/pdb3S9S/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-02 Released: 2012-06-06 
• Deposition Author(s): Lambert, M.H., Xu, R.X.

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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 

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

• PubMed: 21798739 
• 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.

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Organizational Affiliation: 

Neurosciences Centre for Excellence in Drug Discovery, GlaxoSmithKline, New Frontiers Science Park, Harlow, Essex, CM19 5AW, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.67 kDa 
• Atom Count: 2,186 
• Modelled Residue Count: 268 
• Deposited Residue Count: 297 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	284	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B	13	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M0T	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 = 56.086	α = 90
b = 88.754	β = 90
c = 122.605	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Lambert, M.H., Xu, R.X.

Revision History  

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