6DGL

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Darglitazone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Quantitative structural assessment of graded receptor agonism.

Shang, J.Brust, R.Griffin, P.R.Kamenecka, T.M.Kojetin, D.J.

(2019) Proc Natl Acad Sci U S A 116: 22179-22188

  • DOI: 10.1073/pnas.1909016116
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ligand-receptor interactions, which are ubiquitous in physiology, are described by theoretical models of receptor pharmacology. Structural evidence for graded efficacy receptor conformations predicted by receptor theory has been limited but is critic ...

    Ligand-receptor interactions, which are ubiquitous in physiology, are described by theoretical models of receptor pharmacology. Structural evidence for graded efficacy receptor conformations predicted by receptor theory has been limited but is critical to fully validate theoretical models. We applied quantitative structure-function approaches to characterize the effects of structurally similar and structurally diverse agonists on the conformational ensemble of nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ). For all ligands, agonist functional efficacy is correlated to a shift in the conformational ensemble equilibrium from a ground state toward an active state, which is detected by NMR spectroscopy but not observed in crystal structures. For the structurally similar ligands, ligand potency and affinity are also correlated to efficacy and conformation, indicating ligand residence times among related analogs may influence receptor conformation and function. Our results derived from quantitative graded activity-conformation correlations provide experimental evidence and a platform with which to extend and test theoretical models of receptor pharmacology to more accurately describe and predict ligand-dependent receptor activity.


    Organizational Affiliation

    Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
276Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEV
Query on GEV

Download CCD File 
A, B
(5Z)-5-({4-[3-(5-methyl-2-phenyl-1,3-oxazol-4-yl)propanoyl]phenyl}methylidene)-1,3-thiazolidine-2,4-dione
C23 H18 N2 O4 S
DAVUFXMQAAAHHE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.36α = 90
b = 61.74β = 102.72
c = 119.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK101871

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence