5AZT

Ternary complex of hPPARalpha ligand binding domain, 17-oxoDHA and a SRC1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist

Egawa, D.Itoh, T.Akiyama, Y.Saito, T.Yamamoto, K.

(2016) Acs Chem.Biol. --: --

  • DOI: 10.1021/acschembio.6b00338
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 17-Hydroxy docosahexaenoic acid (17-HDHA) is an oxidized form of docosahexaenoic acid (DHA) and known as a specialized proresolving mediator. We found that a further oxidized product, 17-oxodocosahexaenoic acid (17-oxoDHA), activates peroxisome proli ...

    17-Hydroxy docosahexaenoic acid (17-HDHA) is an oxidized form of docosahexaenoic acid (DHA) and known as a specialized proresolving mediator. We found that a further oxidized product, 17-oxodocosahexaenoic acid (17-oxoDHA), activates peroxisome proliferator-activated receptors γ (PPARγ) and PPARα in transcriptional assays and thus can be classified as an α/γ dual agonist. ESI mass spectroscopy and X-ray crystallographic analysis showed that 17-oxoDHA binds to PPARγ and PPARα covalently, making 17-oxoDHA the first of a novel class of PPAR agonists, the PPARα/γ dual covalent agonist. Furthermore, the covalent binding sites were identified as Cys285 for PPARγ and Cys275 for PPARα.


    Organizational Affiliation

    Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor alpha
A, B
269Homo sapiensMutation(s): 1 
Gene Names: PPARA (NR1C1, PPAR)
Find proteins for Q07869 (Homo sapiens)
Go to Gene View: PPARA
Go to UniProtKB:  Q07869
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
15-meric peptide from Nuclear receptor coactivator 1
C
15Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4M5
Query on 4M5

Download SDF File 
Download CCD File 
A, B
(4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid
C22 H32 O3
XXHHYIQPKMKZSU-BBBWWSJWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.253 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.460α = 90.00
b = 59.460β = 90.00
c = 317.940γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Database references