Human PPARgamma in complex with MINCH bound to the AF-2 sub-pocket

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.297 

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Structural basis of the activation of PPAR gamma by the plasticizer metabolites MEHP and MINCH.

Useini, A.Engelberger, F.Kunze, G.Strater, N.

(2023) Environ Int 173: 107822-107822

  • DOI: https://doi.org/10.1016/j.envint.2023.107822
  • Primary Citation of Related Structures:  
    8BF1, 8BF2, 8BFF

  • PubMed Abstract: 

    Di-2-ethylhexyl phthalate (DEHP) and its substitute 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH) are widely used as plasticizers but may have adverse health effects. Via hydrolysis of one of the two ester bonds in the human body, DEHP and DINCH form the monoesters MEHP and MINCH, respectively. Previous studies demonstrated binding of these metabolites to PPARγ and the induction of adipogenesis via this pathway. Detailed structural understanding of how these metabolites interact with PPARγ and thereby affect human health is lacking until now. We therefore characterized the binding modes of MINCH and MEHP to the ligand binding domain of PPARγ by X-ray crystallography and molecular dynamics (MD) simulations. Both compounds bind to the activating function-2 (AF-2) binding site via an interaction of the free carboxylates with the histidines 323 and 449, tyrosine 473 and serine 289. The alkyl chains form hydrophobic interactions with the tunnel next to cysteine 285. These binding modes are generally stable as demonstrated by the MD simulations and they resemble the complexation of fatty acids and their metabolites to the AF-2 site of PPARγ. Similar to the situation for these natural PPARγ agonists, the interaction of the free carboxylate groups of MEHP and MINCH with tyrosine 473 and surrounding residues stabilizes the AF-2 helix in the upward conformation. This state promotes binding of coactivator proteins and thus formation of the active complex for transcription of the specific target genes. Moreover, a comparison of the residues involved in binding of the plasticizer metabolites in vertebrate PPARγ orthologs shows that these compounds likely have similar effects in other species.

  • Organizational Affiliation

    Institute of Bioanalytical Chemistry, Centre for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B, C
283Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QG6 (Subject of Investigation/LOI)
Query on QG6

Download Ideal Coordinates CCD File 
D [auth A](1~{S},2~{R})-2-[(4~{R})-4-methylheptoxy]carbonylcyclohexane-1-carboxylic acid
C16 H28 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.297 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.181α = 90
b = 92.181β = 90
c = 89.509γ = 120
Software Package:
Software NamePurpose
DIALSdata reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1052-Z6

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 2.0: 2023-05-24
    Changes: Non-polymer description, Refinement description
  • Version 2.1: 2024-02-07
    Changes: Data collection, Refinement description