6FX0 | pdb_00006fx0

Structure-based design of Trifarotene (CD5789), a potent and selective RAR gamma agonist for the treatment of acne


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure-based design of Trifarotene (CD5789), a potent and selective RAR gamma agonist for the treatment of acne.

Thoreau, E.Arlabosse, J.M.Bouix-Peter, C.Chambon, S.Chantalat, L.Daver, S.Dumais, L.Duvert, G.Feret, A.Ouvry, G.Pascau, J.Raffin, C.Rodeville, N.Soulet, C.Tabet, S.Talano, S.Portal, T.

(2018) Bioorg Med Chem Lett 28: 1736-1741

  • DOI: https://doi.org/10.1016/j.bmcl.2018.04.036
  • Primary Citation Related Structures: 
    6FX0

  • PubMed Abstract: 

    Retinoids have a dominant role in topical acne therapy and to date, only RARβ and RARγ dual agonists have reached the market. Given the tissue distribution of RAR isoforms, it was hypothesized that developing RARγ -selective agonists could yield a new generation of topical acne treatments that would increase safety margins while maintaining the robust efficacy of previous drugs. Structural knowledge derived from the X-ray structure of known γ-selective CD437, suggested the design of a novel triaryl series of agonists which was optimized and ultimately led to the discovery of Trifarotene/CD5789.


  • Organizational Affiliation
    • Nestlé Skin Health, Les Templiers 2400 Route des Colles, 06410 Biot, France.

Macromolecule Content 

  • Total Structure Weight: 51 kDa 
  • Atom Count: 2,261 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 454 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinoic acid receptor gamma454Homo sapiensMutation(s): 0 
Gene Names: RARGNR1B3
UniProt & NIH Common Fund Data Resources
Find proteins for P13631 (Homo sapiens)
Explore P13631 
Go to UniProtKB:  P13631
PHAROS:  P13631
GTEx:  ENSG00000172819 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13631
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E9T

Query on E9T



Download:Ideal Coordinates CCD File
B [auth A]6-[3-(1-adamantyl)-4-oxidanyl-phenyl]naphthalene-2-carboxylic acid
C27 H26 O3
LDGIHZJOIQSHPB-HYVKCOOLSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
C [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.06α = 90
b = 60.06β = 90
c = 157.82γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references