6KXY

Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives.

Yoshida, T.Oki, H.Doi, M.Fukuda, S.Yuzuriha, T.Tabata, R.Ishimoto, K.Kawahara, K.Ohkubo, T.Miyachi, H.Doi, T.Tachibana, K.

(2020) Sci Rep 10: 7623-7623

  • DOI: 10.1038/s41598-020-64527-x
  • Primary Citation of Related Structures:  
    6KXX, 6KXY

  • PubMed Abstract: 
  • Small-molecule agonism of peroxisome proliferator-activated receptor α (PPARα), a ligand-activated transcriptional factor involved in regulating fatty acid metabolism, is an important approach for treating dyslipidemia. Here, we determined the structures of the ligand-binding domain (LBD) of PPARα in complex with 1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid derivatives, which were recently identified as PPARα-selective activators with markedly different structures from those of the well-known PPARα agonists fibrates ...

    Small-molecule agonism of peroxisome proliferator-activated receptor α (PPARα), a ligand-activated transcriptional factor involved in regulating fatty acid metabolism, is an important approach for treating dyslipidemia. Here, we determined the structures of the ligand-binding domain (LBD) of PPARα in complex with 1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid derivatives, which were recently identified as PPARα-selective activators with markedly different structures from those of the well-known PPARα agonists fibrates. The crystal structures of the complexes showed that they form a canonical hydrogen-bond network involving helix 12 in the LBD, which is thought to be essential for PPARα activation, as also observed for fibrates. However, the phenyl side chain of the compounds occupies a small cavity between Ile272 and Ile354, which is rarely accessed by fibrates. This unique feature may be essential for subtype selectivity and combine with the well-characterized binding mode of fibrates to improve activity. These findings demonstrate the advantage of using 1H-pyrazolo-[3,4-b]pyridine as a skeleton of PPARα agonists and provide insight into the design of molecules for treating dyslipidemia.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor alphaA272Homo 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PGC1alphaB22Homo sapiensMutation(s): 0 
Gene Names: PPARGC1ALEM6PGC1PGC1APPARGC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens)
Explore Q9UBK2 
Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T06 (Subject of Investigation/LOI)
Query on T06

Download Ideal Coordinates CCD File 
C [auth A]6-ethyl-1-(4-fluorophenyl)-3-pentan-3-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid
C20 H22 F N3 O2
IJUSQKANLCHLHY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.548α = 90
b = 61.203β = 90
c = 103.369γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan18H03190

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release