5U3W

Human PPARdelta ligand-binding domain in complexed with specific agonist 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for specific ligation of the peroxisome proliferator-activated receptor delta.

Wu, C.C.Baiga, T.J.Downes, M.La Clair, J.J.Atkins, A.R.Richard, S.B.Fan, W.Stockley-Noel, T.A.Bowman, M.E.Noel, J.P.Evans, R.M.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E2563-E2570

  • DOI: 10.1073/pnas.1621513114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The peroxisome proliferator-activated receptor (PPAR) family comprises three subtypes: PPARα, PPARγ, and PPARδ. PPARδ transcriptionally modulates lipid metabolism and the control of energy homeostasis; therefore, PPARδ agonists are promising agents f ...

    The peroxisome proliferator-activated receptor (PPAR) family comprises three subtypes: PPARα, PPARγ, and PPARδ. PPARδ transcriptionally modulates lipid metabolism and the control of energy homeostasis; therefore, PPARδ agonists are promising agents for treating a variety of metabolic disorders. In the present study, we develop a panel of rationally designed PPARδ agonists. The modular motif affords efficient syntheses using building blocks optimized for interactions with subtype-specific residues in the PPARδ ligand-binding domain (LBD). A combination of atomic-resolution protein X-ray crystallographic structures, ligand-dependent LBD stabilization assays, and cell-based transactivation measurements delineate structure-activity relationships (SARs) for PPARδ-selective targeting and structural modulation. We identify key ligand-induced conformational transitions of a conserved tryptophan side chain in the LBD that trigger reorganization of the H2'-H3 surface segment of PPARδ. The subtype-specific conservation of H2'-H3 sequences suggests that this architectural remodeling constitutes a previously unrecognized conformational switch accompanying ligand-dependent PPARδ transcriptional regulation.


    Organizational Affiliation

    Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037; evans@salk.edu noel@salk.edu.,Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor delta
A, B
272Homo sapiensMutation(s): 0 
Gene Names: PPARD (NR1C2, PPARB)
Find proteins for Q03181 (Homo sapiens)
Go to Gene View: PPARD
Go to UniProtKB:  Q03181
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B7G
Query on B7G

Download SDF File 
Download CCD File 
A
HEPTYL-BETA-D-GLUCOPYRANOSIDE
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N
 Ligand Interaction
7U1
Query on 7U1

Download SDF File 
Download CCD File 
A, B
6-(2-{[([1,1'-biphenyl]-4-carbonyl)(cyclopropyl)amino]methyl}phenoxy)hexanoic acid
C29 H31 N O4
XWRSFMVWMRKGCC-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

Download SDF File 
Download CCD File 
A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.560α = 90.00
b = 94.810β = 98.27
c = 96.610γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references
  • Version 1.2: 2017-04-05
    Type: Database references