X-ray crystal structure of PPAR gamma ligand binding domain in complex with CZ39

Experimental Data Snapshot

  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

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This is version 1.2 of the entry. See complete history


Biological Screening and Crystallographic Studies of Hydroxy gamma-Lactone Derivatives to Investigate PPAR gamma Phosphorylation Inhibition.

Capelli, D.Cazzaniga, G.Mori, M.Laghezza, A.Loiodice, F.Quaglia, M.Negro, E.Meneghetti, F.Villa, S.Montanari, R.

(2023) Biomolecules 13

  • DOI: https://doi.org/10.3390/biom13040694
  • Primary Citation of Related Structures:  
    8ADF, 8C0C

  • PubMed Abstract: 

    PPARγ represents a key target for the treatment of type 2 diabetes and metabolic syndrome. To avoid serious adverse effects related to the PPARγ agonism profile of traditional antidiabetic drugs, a new opportunity is represented by the development of molecules acting as inhibitors of PPARγ phosphorylation by the cyclin-dependent kinase 5 (CDK5). Their mechanism of action is mediated by the stabilization of the PPARγ β-sheet containing Ser273 (Ser245 in PPARγ isoform 1 nomenclature). In this paper, we report the identification of new γ-hydroxy-lactone-based PPARγ binders from the screening of an in-house library. These compounds exhibit a non-agonist profile towards PPARγ, and one of them prevents Ser245 PPARγ phosphorylation by acting mainly on PPARγ stabilization and exerting a weak CDK5 inhibitory effect.

  • Organizational Affiliation

    Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Strada Provinciale 35d, n. 9-00010, Montelibretti, 34149 Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
303Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  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
Query on LRA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C16 H11 Br O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.878α = 90
b = 59.954β = 103.29
c = 117.37γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description