9HX2 | pdb_00009hx2

X-ray crystal structure of PPAR gamma Ligand Binding Domain in complex with CZ58


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.282 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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Literature

Enhancing the activity of gamma-hydroxy lactone derivatives as innovative peroxisome proliferator-activated receptor gamma non-agonists inhibiting cyclin-dependent kinase 5-mediated phosphorylation.

Cazzaniga, G.Capelli, D.Montanari, R.Fassi, E.M.A.Grazioso, G.Tresoldi, A.Rinaldi, F.Calleri, E.Bassanini, I.Romeo, S.Garofalo, M.Mori, M.Meneghetti, F.Villa, S.

(2025) Eur J Med Chem 292: 117657-117657

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117657
  • Primary Citation of Related Structures:  
    9HX2

  • PubMed Abstract: 

    Insulin resistance (IR) is a pathological condition in which tissues exhibit a reduced response to normal or elevated levels of insulin. Type 2 diabetes mellitus (T2DM) and Metabolic Syndrome are the most prevalent disorders associated with IR. Most of the glitazones, traditional anti-diabetic drugs acting as Peroxisome Proliferator-Activated Receptor γ (PPARγ) agonists, have been withdrawn from the market. To mitigate the serious adverse effects associated with PPARγ agonism, a new opportunity is represented by the 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 Ser245. Recently, we identified 4-(4-bromophenyl)-3-hydroxy-5-(3-hydroxyphenyl)furan-2(5H)-one (I) as a PPARγ non-agonist, capable of blocking the phosphorylation of the enzyme without direct effects on either CDK5 or PPARγ. Here, we isolated the two enantiomers of I, unambiguously defined their absolute configuration through single crystal X-ray diffraction and demonstrated by Grating-Coupled Interferometry binding assays that both (S)-I and (R)-I exhibited comparable affinity for PPARγ. Then, a library of 12 analogs was designed through structure-based modifications, optimizing the interactions within the ligand-binding domain. GCI analysis identified derivative 11, featuring an oxyacetic group in place of the initial hydroxyl function of the reference compound I, as the most promising candidate (K D  = 186 nM). The crystal structure of the PPARγ-LBD/11 complex revealed a hydrogen bond interaction with Arg280, further stabilizing the binding conformation. These findings highlight the potential of γ-hydroxy lactone derivatives as PPARγ modulators and provide a foundation for future drug development targeting IR.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy; Department of Science and High Technology, University of Insubria, via Valleggio 9, 22100, Como, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
286Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IYE
Query on A1IYE

Download Ideal Coordinates CCD File 
C [auth A]2-[3-[(2~{R})-3-(4-bromophenyl)-4-oxidanyl-5-oxidanylidene-2~{H}-furan-2-yl]phenoxy]ethanoic acid
C18 H13 Br O6
UWLVUUWPNDCOQR-QGZVFWFLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.282 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.196α = 90
b = 61.182β = 102.39
c = 118.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
AMoREphasing

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: 2025-05-14
    Type: Initial release