3AN4

Human PPAR gamma ligand binding domain in complex with a gamma selective agonist MO4R

• PDB DOI: https://doi.org/10.2210/pdb3AN4/pdb

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


• Deposited: 2010-08-30 Released: 2011-07-27 
• Deposition Author(s): Oyama, T., Ohashi, M., Waku, T., Miyachi, H., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 

Starting Model: experimental

Literature

Design, Synthesis, and Structural Analysis of Phenylpropanoic Acid-Type PPAR gamma-Selective Agonists: Discovery of Reversed Stereochemistry-Activity Relationship

Ohashi, M., Oyama, T., Nakagome, I., Satoh, M., Nishio, Y., Nobusada, H., Hirono, S., Morikawa, K., Hashimoto, Y., Miyachi, H.

(2011) J Med Chem 54: 331-341

• PubMed: 21128600 
• DOI: https://doi.org/10.1021/jm101233f
• Primary Citation of Related Structures:  
  3AN3, 3AN4


• PubMed Abstract: 
  

  Peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-mediated transcription factor with roles in glucose, lipid, and lipoprotein homeostasis, and PPARγ ligands are expected have therapeutic potential in these as well as other areas. We report here the design, synthesis, crystallographic analysis, and computational studies of α-benzylphenylpropanoic acid PPARγ agonists. Interestingly, these compounds show a reversal of the stereochemistry-transactivation activity relationship observed with other phenylpropanoic acid ligands.

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Organizational Affiliation: 

Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.63 kDa 
• Atom Count: 4,273 
• Modelled Residue Count: 519 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	286	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 GTEx:  ENSG00000132170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M7R	C [auth A]	(2R)-2-benzyl-3-(4-propoxy-3-{[({4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]phenyl}carbonyl)amino]methyl}phenyl)propanoic acid C37 H43 N O4 XYMQLACGAYNBRX-FJRQOFADSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M7R	BindingDB:  3AN4	EC50: 3.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.391	α = 90
b = 61.271	β = 102.82
c = 118.871	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Oyama, T., Ohashi, M., Waku, T., Miyachi, H., Morikawa, K.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description