5Y7X

Human Peroxisome proliferator-activated receptor (PPAR) delta in complexed with a potent and selective agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Highly potent and selective PPAR delta agonist reverses memory deficits in mouse models of Alzheimer's disease.

Kim, H.J.Kim, H.Song, J.Hong, J.Y.Lee, E.H.Londhe, A.M.Choi, J.W.Park, S.J.Oh, E.Yoon, H.Hwang, H.Hahn, D.Jung, K.Kwon, S.Kadayat, T.M.Ma, M.J.Joo, J.Kim, J.Bae, J.H.Hwang, H.Pae, A.N.Cho, S.J.Park, J.H.Chin, J.Kang, H.Park, K.D.

(2024) Theranostics 14: 6088-6108

  • DOI: https://doi.org/10.7150/thno.96707
  • Primary Citation of Related Structures:  
    5Y7X

  • PubMed Abstract: 

    Rationale: Alzheimer's disease (AD) is a progressive neurodegenerative disease accompanied by neurotoxicity, excessive inflammation, and cognitive impairment. The peroxisome proliferator-activated receptor (PPAR) δ is a potential target for AD. However, its regulatory mechanisms and therapeutic potential in AD remain unclear. We aimed to investigate if the activation of PPARδ using a highly selective and potent agonist could provide an effective therapeutic strategy against AD. Methods: We synthesized a novel PPARδ agonist, 5a, containing a selenazole group and determined the X-ray crystal structure of its complex with PPARδ. The drug-like properties of 5a were assessed by analyzing cytochrome P450 (CYP) inhibition, microsomal stability, pharmacokinetics, and mutagenicity. We investigated the anti-inflammatory effects of 5a using lipopolysaccharide (LPS)-stimulated BV-2 microglia and neuroinflammatory mouse model. The therapeutic efficacy of 5a was evaluated in AD mice with scopolamine-induced memory impairment and APP/PS1 by analyzing cognitive function, glial reactivity, and amyloid pathology. Results: Compound 5a , the most potent and selective PPARδ agonist, was confirmed to bind hPPARδ in a complex by X-ray crystallographic analysis. PPARδ activation using 5a showed potent anti-inflammatory effects in activated glial cells and mouse model of neuroinflammation. Administration of 5a inhibited amyloid plaque deposition by suppressing the expression of neuronal beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), and reduced abnormal glial hyperactivation and inflammatory responses, resulting in improved learning and memory in the APP/PS1 mouse model of AD. Conclusion: We identified that specific activation of PPARδ provides therapeutic effects on multiple pathogenic phenotypes of AD, including neuroinflammation and amyloid deposition. Our findings suggest the potential of PPARδ as a promising drug target for treating AD.


  • Organizational Affiliation

    Center for Brain Disorders, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor delta
A, B
292Homo 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
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8RR
Query on 8RR

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
2-[2-methyl-4-[[4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-selenazol-5-yl]methylsulfanyl]phenoxy]ethanoic acid
C21 H18 F3 N O3 S Se
FLCJPWUNOIWRCO-UHFFFAOYSA-N
JZR
Query on JZR

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
hexyl beta-D-glucopyranoside
C12 H24 O6
JVAZJLFFSJARQM-RMPHRYRLSA-N
PGO
Query on PGO

Download Ideal Coordinates CCD File 
F [auth A]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
K
Query on K

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D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.766α = 90
b = 93.896β = 97.4
c = 96.871γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
PHENIXphasing
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Database references, Structure summary