8HF8 | pdb_00008hf8

Human PPAR delta ligand binding domain in complex with a synthetic agonist V1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LOOClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Discovery of the First Subnanomolar PPAR alpha / delta Dual Agonist for the Treatment of Cholestatic Liver Diseases.

Feng, Z.Xiang, J.Sun, G.Liu, H.Wang, Y.Liu, X.Feng, J.Xu, Q.Wen, X.Yuan, H.Sun, H.Dai, L.

(2023) J Med Chem 66: 7331-7354

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c02123
  • Primary Citation of Related Structures:  
    8HF8

  • PubMed Abstract: 

    Peroxisome proliferator-activator receptors α/δ (PPARα/δ) are considered as potential drug targets for cholestatic liver diseases (CLD) via ameliorating hepatic cholestasis, inflammation, and fibrosis. In this work, we developed a series of hydantoin derivatives as potent PPARα/δ dual agonists. Representative compound V1 exhibited PPARα/δ dual agonistic activity at the subnanomolar level (PPARα EC 50 = 0.7 nM; PPARδ EC 50 = 0.4 nM) and showed excellent selectivity over other related nuclear receptors. The crystal structure revealed the binding mode of V1 and PPARδ at 2.1 Å resolution. Importantly, V1 demonstrated excellent pharmacokinetic (PK) properties and a good safety profile. Notably, V1 showed potent anti-CLD and antifibrotic effects in preclinical models at very low doses (0.03 and 0.1 mg/kg). Collectively, this work provides a promising drug candidate for treating CLD and other hepatic fibrosis diseases.


  • Organizational Affiliation

    Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor delta
A, B
282Homo sapiensMutation(s): 0 
Gene Names: PPARDNR1C2PPARB
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
PHAROS:  Q03181
GTEx:  ENSG00000112033 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03181
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.795α = 90
b = 92.966β = 96
c = 96.715γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LOOClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release