9T5S | pdb_00009t5s

Crystal structure of human PPARalpha in complex with co-activator PGC-1 alpha peptide and bempedoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.211 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Bempedoic acid directly binds and activates PPAR alpha.

Papa, C.Rose, A.Martin, H.N.G.Useini, A.Geier, F.Liao, L.Rodriguez-Aguilera, J.R.Valina-Allo, P.Hoffmann, A.Tvardovskiy, A.Zulfqar, F.Zimmerman, A.Schicht, G.Ott, F.Korner, C.Engelmann, B.Rolle-Kampczyk, U.von Bergen, M.Meier, M.Bartke, T.Seehofer, D.Kloting, N.Matz-Soja, M.Damm, G.Boeckel, J.N.Buescher, J.M.Bluher, M.Laufs, U.Bondareva, O.Strater, N.Kunze, G.Heiker, J.T.Sheikh, B.N.

(2026) Cell Metab 

  • DOI: https://doi.org/10.1016/j.cmet.2025.12.018
  • Primary Citation Related Structures: 
    9T5S

  • PubMed Abstract: 

    Bempedoic acid (BA) is a recently approved drug that lowers cholesterol and hepatic lipids, yet its mechanism of action remains incompletely understood. Here, we combine transcriptomic, biochemical, and structural approaches to show that BA directly binds to and activates peroxisome proliferator-activated receptor alpha (PPARα). BA treatment robustly induced PPARα signaling and fatty acid oxidation in primary hepatocytes and mouse liver. Through X-ray crystallography, we uncovered that BA binds to the ligand-binding domain of PPARα and stabilizes its active conformation. BA activated PPARα target genes independently of very-long-chain acyl-coenzyme A (CoA) synthetase (ACSVL1), the liver-enriched enzyme that converts BA to its bempedoyl-CoA form. Notably, BA-mediated induction of fatty acid oxidation required PPARα. Together, this work reveals direct PPARα activation as a key mechanism of BA action, providing a molecular basis for its lipid-lowering effects and suggesting broader therapeutic potential beyond the liver.


  • Organizational Affiliation
    • Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), Helmholtz Center Munich, 04103 Leipzig, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor alpha
A, C
290Homo sapiensMutation(s): 0 
Gene Names: PPARANR1C1PPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
PHAROS:  Q07869
GTEx:  ENSG00000186951 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07869
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
B, D
19Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens)
Explore Q9UBK2 
Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2
GTEx:  ENSG00000109819 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBK2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.211 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.253α = 90
b = 99.748β = 99.8
c = 61.612γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany457240345
Helmholtz AssociationGermany--
German Research Foundation (DFG)Germany209933838

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references