2F4B

Crystal structure of the ligand binding domain of human PPAR-gamma in complex with an agonist

• PDB DOI: https://doi.org/10.2210/pdb2F4B/pdb

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


• Deposited: 2005-11-23 Released: 2006-02-14 
• Deposition Author(s): Lu, I.L., Peng, Y.H., Mahindroo, N., Hsieh, H.P., Wu, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.288 (Depositor) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Indol-1-yl Acetic Acids as Peroxisome Proliferator-Activated Receptor Agonists: Design, Synthesis, Structural Biology, and Molecular Docking Studies

Mahindroo, N., Wang, C.C., Liao, C.C., Huang, C.F., Lu, I.L., Lien, T.W., Peng, Y.H., Huang, W.J., Lin, Y.T., Hsu, M.C., Lin, C.H., Tsai, C.H., Hsu, J.T., Chen, X., Lyu, P.C., Chao, Y.S., Wu, S.Y., Hsieh, H.P.

(2006) J Med Chem 49: 1212-1216

• PubMed: 16451087 
• DOI: https://doi.org/10.1021/jm0510373
• Primary Citation of Related Structures:  
  2F4B


• PubMed Abstract: 
  

  A series of novel indole-based PPAR agonists is described leading to discovery of 10k, a highly potent PPAR pan-agonist. The structural biology and molecular docking studies revealed that the distances between the acidic group and the linker, when a ligand was complexed with PPARgamma protein, were important for the potent activity. The hydrophobic tail part of 10k makes intensive hydrophobic interaction with the PPARgamma protein resulting in potent activity.

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Organizational Affiliation: 

Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, Republic of China.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 62.52 kDa 
• Atom Count: 4,535 
• Modelled Residue Count: 542 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	271	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EHA	C [auth A]	(5-{3-[(6-BENZOYL-1-PROPYL-2-NAPHTHYL)OXY]PROPOXY}-1H-INDOL-1-YL)ACETIC ACID C33 H31 N O5 ZXWVCCFKIRBLDP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EHA	BindingDB:  2F4B	IC50: 50 (nM) from 1 assay(s)
		EC50: 70 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.288 (Depositor) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.967	α = 90
b = 88.642	β = 90.01
c = 57.878	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Lu, I.L., Peng, Y.H., Mahindroo, N., Hsieh, H.P., Wu, S.Y.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations