4JYG

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 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 RARα, β and γ. Multiple studies support that RARβ possesses functional characteristics of a tumor suppressor and indeed, its expression is frequently lost in neoplastic tissues ...

    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 RARα, β and γ. Multiple studies support that RARβ possesses functional characteristics of a tumor suppressor and indeed, its expression is frequently lost in neoplastic tissues. However, it has been recently reported that RARβ 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 RARβ-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 RARβ-selective ligand exhibiting a full transcriptional agonistic activity and activating RARβ as efficiently as the reference agonist TTNPB. In addition, we solved the crystal structures of the RARβ 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 RARα antagonist and an RARβ full agonist, and revealed the structural basis of partial agonism. Finally, in addition to revealing that a flip by 180° of the amide linker, that usually confers RARα selectivity, accounts for the RARβ selectivity of BMS948, the structural analysis uncovers guidelines for the rational design of RARβ-selective antagonists.


    Organizational Affiliation

    Inserm U1054, Centre de Biochimie Structurale, Montpellier, France; CNRS UMR5048, Universités Montpellier 1 & 2, Montpellier, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor betaA, B267Homo 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
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Steroid Receptor Coactivator 1C [auth F], D [auth G]13Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1NY (Subject of Investigation/LOI)
Query on 1NY

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid
C26 H23 N O3
AZQWAFBHDUNJHM-UHFFFAOYSA-N
 Ligand Interaction
PE4
Query on PE4

Download Ideal Coordinates CCD File 
F [auth B]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
H [auth G]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.24α = 90
b = 84.83β = 90
c = 108.42γ = 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