5U45

Human PPARdelta ligand-binding domain in complexed with specific agonist 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report



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:  
    5U41, 5U40, 5U3R, 5U43, 5U3Q, 5U42, 5U3T, 5U45, 5U3S, 5U44

  • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor deltaAB272Homo sapiensMutation(s): 0 
Gene Names: PPARDNR1C2PPARB
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
NIH Common Fund Data Resources
PHAROS  Q03181
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7SY
Query on 7SY

Download CCD File 
A, B
6-(2-{[cyclopropyl(3'-fluoro[1,1'-biphenyl]-4-carbonyl)amino]methyl}phenoxy)hexanoic acid
C29 H30 F N O4
MNZOAOAVCAPVOP-UHFFFAOYSA-N
 Ligand Interaction
B7G
Query on B7G

Download CCD File 
A, B
heptyl beta-D-glucopyranoside
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N
 Ligand Interaction
PEG
Query on PEG

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

Download CCD File 
A, B
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.53α = 90
b = 95.26β = 97.56
c = 96.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 1.2: 2017-04-05
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary