Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 34.54 kDa 
• Atom Count: 2316 
• Modelled Residue Count: 274 
• Deposited Residue Count: 299 
• Unique protein chains: 2

5YCP

Human PPARgamma ligand binding domain complexed with Rosiglitazone

• PDB 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
• Primary Citation of Related Structures:  
  5YCN, 5YCP


• 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	Image
Peroxisome proliferator-activated receptor gamma	A	283	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
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	16	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
BRL	C [auth A]	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) C18 H19 N3 O3 S YASAKCUCGLMORW-HNNXBMFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BRL	BindingDB:  5YCP	Ki: min: 8, max: 59 (nM) from 5 assay(s)
		Kd: min: 0.14, max: 48 (nM) from 3 assay(s)
		IC50: min: 1, max: 298 (nM) from 10 assay(s)
		EC50: min: 1, max: 1600 (nM) from 35 assay(s)

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