Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 34.54 kDa 
• Atom Count: 2316 
• Residue Count: 274 
• Unique protein chains: 2

5YCP

Human PPARgamma ligand binding domain complexed with Rosiglitazone

• DOI: 10.2210/pdb5YCP/pdb

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


• Deposited: 2017-09-07 Released: 2018-09-12 
• Deposition Author(s): Jang, J.Y., Han, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Structural Basis for the Enhanced Anti-Diabetic Efficacy of Lobeglitazone on PPAR gamma.

Jang, J.Y., Bae, H., Lee, Y.J., Choi, Y.I., Kim, H.J., Park, S.B., Suh, S.W., Kim, S.W., Han, B.W.

(2018) Sci Rep 8: 31-31

• PubMed: 29311579 
• DOI: 10.1038/s41598-017-18274-1
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Peroxisome proliferator-activated receptor γ (PPARγ) is a member of the nuclear receptor superfamily. It functions as a ligand-activated transcription factor and plays important roles in the regulation of adipocyte differentiation, insulin resistance, and inflammation. Here, we report the crystal structures of PPARγ in complex with lobeglitazone, a novel PPARγ agonist, and with rosiglitazone for comparison. The thiazolidinedione (TZD) moiety of lobeglitazone occupies the canonical ligand-binding pocket near the activation function-2 (AF-2) helix (i.e., helix H12) in ligand-binding domain as the TZD moiety of rosiglitazone does. However, the elongated p-methoxyphenol moiety of lobeglitazone interacts with the hydrophobic pocket near the alternate binding site of PPARγ. The extended interaction of lobeglitazone with the hydrophobic pocket enhances its binding affinity and could affect the cyclin-dependent kinase 5 (Cdk5)-mediated phosphorylation of PPARγ at Ser245 (in PPARγ1 numbering; Ser273 in PPARγ2 numbering). Lobeglitazone inhibited the phosphorylation of PPARγ at Ser245 in a dose-dependent manner and exhibited a better inhibitory effect on Ser245 phosphorylation than rosiglitazone did. Our study provides new structural insights into the PPARγ regulation by TZD drugs and could be useful for the discovery of new PPARγ ligands as an anti-diabetic drug, minimizing known side effects.

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Organizational Affiliation: 

Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peroxisome proliferator-activated receptor gamma	A	283	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens) Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231 GTEx  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nuclear receptor coactivator 1	B	16	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens) 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
BRL	A	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) C18 H19 N3 O3 S YASAKCUCGLMORW-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.809	α = 90
b = 53.133	β = 90
c = 54.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-09-07 
• Released Date: 2018-09-12 
Deposition Author(s): Jang, J.Y., Han, B.W.

Revision History 

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references