4DQM

Revealing a marine natural product as a novel agonist for retinoic acid receptors with a unique binding mode and antitumor activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Revealing a natural marine product as a novel agonist for retinoic acid receptors with a unique binding mode and inhibitory effects on cancer cells.

Wang, S.Wang, Z.Lin, S.Zheng, W.Wang, R.Jin, S.Chen, J.Jin, L.Li, Y.

(2012) Biochem J 446: 79-87

  • DOI: 10.1042/BJ20120726
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Retinoids display anti-tumour activity on various cancer cells and therefore have been used as important therapeutic agents. However, adverse side effects and RA (retinoic acid) resistance limit further development and clinical application of retinoi ...

    Retinoids display anti-tumour activity on various cancer cells and therefore have been used as important therapeutic agents. However, adverse side effects and RA (retinoic acid) resistance limit further development and clinical application of retinoid-based therapeutic agents. We report in the present paper the identification of a natural marine product that activates RARs (RA receptors) with a chemical structure distinct from retinoids by high-throughput compound library screening. Luffariellolide was uncovered as a novel RAR agonist by inducing co-activator binding to these receptors in vitro, further inhibiting cell growth and regulating RAR target genes in various cancer cells. Structural and molecular studies unravelled a unique binding mode of this natural ligand to RARs with an unexpected covalent modification on the RAR. Functional characterization further revealed that luffariellolide displays chemotherapeutic potentials for overcoming RA resistance in colon cancer cells, suggesting that luffariellolide may represent a unique template for designing novel non-retinoid compounds with advantages over current RA drugs.


    Organizational Affiliation

    State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Fujian 361005, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor alpha
A, C
234Homo sapiensMutation(s): 0 
Gene Names: NR1B1RARA
Find proteins for P10276 (Homo sapiens)
Go to UniProtKB:  P10276
NIH Common Fund Data Resources
PHAROS  P10276
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B, D
10Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LUF
Query on LUF

Download CCD File 
A, C
(5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethylcyclohex-1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxyfuran-2(5H)-one
C25 H38 O3
JPWPYTMXSXYUPG-XKILHPSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.12α = 90
b = 104.46β = 90
c = 113.48γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Experimental preparation
  • Version 1.2: 2017-11-15
    Changes: Advisory, Refinement description