Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.87 kDa 
• Atom Count: 4615 
• Residue Count: 535 
• Unique protein chains: 2

3T03

Crystal structure of PPAR gamma ligand binding domain in complex with a novel partial agonist GQ-16

• DOI: 10.2210/pdb3T03/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION REGULATOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-07-19 Released: 2012-05-23 
• Deposition Author(s): Rajagopalan, S., Webb, P., Baxter, J.D., Brennan, R.G., Phillips, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.247 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 

Literature

GQ-16, a novel peroxisome proliferator-activated receptor (PPAR gamma) ligand, promotes insulin sensitization without weight gain.

Amato, A.A., Rajagopalan, S., Lin, J.Z., Carvalho, B.M., Figueira, A.C., Lu, J., Ayers, S.D., Mottin, M., Silveira, R.L., Souza, P.C., Mourao, R.H., Saad, M.J., Togashi, M., Simeoni, L.A., Abdalla, D.S., Skaf, M.S., Polikparpov, I., Lima, M.C., Galdino, S.L., Brennan, R.G., Baxter, J.D., Pitta, I.R., Webb, P., Phillips, K.J., Neves, F.A.

(2012) J Biol Chem 287: 28169-28179

• PubMed: 22584573 
• DOI: 10.1074/jbc.M111.332106
• Primary Citation of Related Structures:  
  3T03


• PubMed Abstract: 
  

The recent discovery that peroxisome proliferator-activated receptor γ (PPARγ) targeted anti-diabetic drugs function by inhibiting Cdk5-mediated phosphorylation of the receptor has provided a new viewpoint to evaluate and perhaps develop improved insulin-sensitizing agents. Herein we report the development of a novel thiazolidinedione that retains similar anti-diabetic efficacy as rosiglitazone in mice yet does not elicit weight gain or edema, common side effects associated with full PPARγ activation. Further characterization of this compound shows GQ-16 to be an effective inhibitor of Cdk5-mediated phosphorylation of PPARγ. The structure of GQ-16 bound to PPARγ demonstrates that the compound utilizes a binding mode distinct from other reported PPARγ ligands, although it does share some structural features with other partial agonists, such as MRL-24 and PA-082, that have similarly been reported to dissociate insulin sensitization from weight gain. Hydrogen/deuterium exchange studies reveal that GQ-16 strongly stabilizes the β-sheet region of the receptor, presumably explaining the compound's efficacy in inhibiting Cdk5-mediated phosphorylation of Ser-273. Molecular dynamics simulations suggest that the partial agonist activity of GQ-16 results from the compound's weak ability to stabilize helix 12 in its active conformation. Our results suggest that the emerging model, whereby "ideal" PPARγ-based therapeutics stabilize the β-sheet/Ser-273 region and inhibit Cdk5-mediated phosphorylation while minimally invoking adipogenesis and classical agonism, is indeed a valid framework to develop improved PPARγ modulators that retain antidiabetic actions while minimizing untoward effects.

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Organizational Affiliation: 

Laboratório de Farmacologia Molecular, Departamento de Ciências Farmacêuticas, Faculdade de Ciências da Saúde, Universidade de Brasília, 70919-970 Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	284	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231 GTEx  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	C, D	18	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788 GTEx  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3T0	A, B	(5Z)-5-(5-bromo-2-methoxybenzylidene)-3-(4-methylbenzyl)-1,3-thiazolidine-2,4-dione C19 H16 Br N O3 S AMLZLORVKZAHOH-YVLHZVERSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
3T0	Ki :  160   nM  PDBBind
3T0	Ki:  160   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.247 
• R-Value Work: 0.208 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.69	α = 90
b = 84.39	β = 90
c = 96.98	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-19 
• Released Date: 2012-05-23 
Deposition Author(s): Rajagopalan, S., Webb, P., Baxter, J.D., Brennan, R.G., Phillips, K.J.

Revision History 

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references