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 6QJ5 | pdb_00006qj5

X-ray structure of PPARgamma LBD with the ligand NV1380


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

A Novel N-Substituted Valine Derivative with Unique Peroxisome Proliferator-Activated Receptor gamma Binding Properties and Biological Activities.

Peiretti, F., Montanari, R., Capelli, D., Bonardo, B., Colson, C., Amri, E.Z., Grimaldi, M., Balaguer, P., Ito, K., Roeder, R.G., Pochetti, G., Brunel, J.M.

(2020) J Med Chem 63: 13124-13139

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01555
  • Primary Citation Related Structures: 
    6QJ5, 6ZLY

  • PubMed Abstract: 

    A proprietary library of novel N -aryl-substituted amino acid derivatives bearing a hydroxamate head group allowed the identification of compound 3a that possesses weak proadipogenic and peroxisome proliferator-activated receptor γ (PPARγ) activating properties. The systematic optimization of 3a , in order to improve its PPARγ agonist activity, led to the synthesis of compound 7j ( N -aryl-substituted valine derivative) that possesses dual PPARγ/PPARα agonistic activity. Structural and kinetic analyses reveal that 7j occupies the typical ligand binding domain of the PPARγ agonists with, however, a unique high-affinity binding mode. Furthermore, 7j is highly effective in preventing cyclin-dependent kinase 5-mediated phosphorylation of PPARγ serine 273. Although less proadipogenic than rosiglitazone, 7j significantly increases adipocyte insulin-stimulated glucose uptake and efficiently promotes white-to-brown adipocyte conversion. In addition, 7j prevents oleic acid-induced lipid accumulation in hepatoma cells. The unique biochemical properties and biological activities of compound 7j suggest that it would be a promising candidate for the development of compounds to reduce insulin resistance, obesity, and nonalcoholic fatty liver disease.


  • Organizational Affiliation: 
    • Aix Marseille University, INSERM, INRAE, C2VN, 13385 Marseille, France.

Macromolecule Content 

  • Total Structure Weight: 69.52 kDa 
  • Atom Count: 4,161 
  • Modeled Residue Count: 499 
  • Deposited Residue Count: 608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
304Homo sapiensMutation(s): 0 
Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H8R
(Subject of Investigation/LOI)

Query on H8R



Download:Ideal Coordinates CCD File
C [auth A](2~{S})-3-methyl-2-[(4-octoxyphenyl)carbonylamino]butanoic acid
C20 H31 N O4
JIIPBCFIUGBDHZ-SFHVURJKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
H8R BindingDB:  6QJ5 Kd: 30 (nM) from 1 assay(s)
IC50: min: 956, max: 2248 (nM) from 2 assay(s)
EC50: min: 400, max: 1484 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.6α = 90
b = 61.94β = 103
c = 119.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description