5WR1

Covalent bond formation of bifunctional ligand with hPPARg-LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

On-site reaction for PPAR gamma modification using a specific bifunctional ligand

Kojima, H.Itoh, T.Yamamoto, K.

(2017) Bioorg Med Chem 25: 6492-6500

  • DOI: https://doi.org/10.1016/j.bmc.2017.10.024
  • Primary Citation of Related Structures:  
    5WQX, 5WR0, 5WR1

  • PubMed Abstract: 

    Site-specific labeling is an important methodology to elucidate the biological function of a target protein. Here, we report a strategy for site-specific chemical labeling, termed the "on-site reaction". We designed and readily synthesized a bifunctional ligand possessing two reaction sites, an enone and an azide moiety. This strategy involves an on-site conjugate addition reaction with protein followed by a Hüisgen cycloaddition reaction. We demonstrate this strategy by using fluorescein as a probe and peroxisome proliferator activated receptor γ (PPARγ) as a target protein. The reactions were evaluated by ESI-mass analysis and the binding site and modes of binding were revealed by X-ray crystallization analysis. The proposed methodology can easily convert a covalent ligand into chemical tool for protein functional analysis and the identification of drug targets.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
276Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
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
8XO
Query on 8XO

Download Ideal Coordinates CCD File 
C [auth A]2-[E-(E-16-azido-2-oxidanylidene-hexadec-3-enylidene)amino]ethanoic acid
C18 H30 N4 O3
VMJXHBQSQBKHEB-PZBCRXGTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93α = 90
b = 61.43β = 102.85
c = 118.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary