4JYG | pdb_00004jyg

Crystal structure of RARbeta LBD in complex with agonist BMS411 [4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 ?
  • R-Value Free: 
    0.257 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor beta (RAR beta , NR1B2) Selective Agonist.

Nadendla, E.Teyssier, C.Delfosse, V.Vivat, V.Krishnasamy, G.Gronemeyer, H.Bourguet, W.Germain, P.

(2015) PLoS One 10: e0123195-e0123195

  • DOI: https://doi.org/10.1371/journal.pone.0123195
  • Primary Citation of Related Structures:  
    4JYG, 4JYH, 4JYI

  • PubMed Abstract: 

    Retinoic acid is an important regulator of cell differentiation which plays major roles in embryonic development and tissue remodeling. The biological action of retinoic acid is mediated by three nuclear receptors denoted RAR¦Á, ¦Â and ¦Ã. Multiple studies support that RAR¦Â possesses functional characteristics of a tumor suppressor and indeed, its expression is frequently lost in neoplastic tissues. However, it has been recently reported that RAR¦Â could also play a role in mammary gland tumorigenesis, thus demonstrating the important but yet incompletely understood function of this receptor in cancer development. As a consequence, there is a great need for RAR¦Â-selective agonists and antagonists as tools to facilitate the pharmacological analysis of this protein in vitro and in vivo as well as for potential therapeutic interventions. Here we provide experimental evidences that the novel synthetic retinoid BMS948 is an RAR¦Â-selective ligand exhibiting a full transcriptional agonistic activity and activating RAR¦Â as efficiently as the reference agonist TTNPB. In addition, we solved the crystal structures of the RAR¦Â ligand-binding domain in complex with BMS948 and two related compounds, BMS641 and BMS411. These structures provided a rationale to explain how a single retinoid can be at the same time an RAR¦Á antagonist and an RAR¦Â full agonist, and revealed the structural basis of partial agonism. Finally, in addition to revealing that a flip by 180¡ã of the amide linker, that usually confers RAR¦Á selectivity, accounts for the RAR¦Â selectivity of BMS948, the structural analysis uncovers guidelines for the rational design of RAR¦Â-selective antagonists.


  • Organizational Affiliation

    Inserm U1054, Centre de Biochimie Structurale, Montpellier, France; CNRS UMR5048, Universit¨¦s Montpellier 1 & 2, Montpellier, France; CAS in Crystallography and Biophysics, University of Madras, Chennai, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor beta
A, B
267Homo sapiensMutation(s): 0 
Gene Names: RARBHAPNR1B2
UniProt & NIH Common Fund Data Resources
Find proteins for P10826 (Homo sapiens)
Explore P10826 
Go to UniProtKB:  P10826
PHAROS:  P10826
GTEx:  ENSG00000077092 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10826
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid Receptor Coactivator 1C [auth F],
D [auth G]
13Homo sapiensMutation(s): 0 
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 ?
  • R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 58.24¦Á = 90
b = 84.83¦Â = 90
c = 108.42¦Ã = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
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