Crystal structure of the RAR alpha ligand-binding domain in complex with an antagonist

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Identification of potent and selective retinoic acid receptor gamma (RAR gamma ) antagonists for the treatment of osteoarthritis pain using structure based drug design.

Hughes, N.E.Bleisch, T.J.Jones, S.A.Richardson, T.I.Doti, R.A.Wang, Y.Stout, S.L.Durst, G.L.Chambers, M.G.Oskins, J.L.Lin, C.Adams, L.A.Page, T.J.Barr, R.J.Zink, R.W.Osborne, H.Montrose-Rafizadeh, C.Norman, B.H.

(2016) Bioorg Med Chem Lett 26: 3274-3277

  • DOI: https://doi.org/10.1016/j.bmcl.2016.05.056
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A series of triaryl pyrazoles were identified as potent pan antagonists for the retinoic acid receptors (RARs) α, β and γ. X-ray crystallography and structure-based drug design were used to improve selectivity for RARγ by targeting residue differences in the ligand binding pockets of these receptors. This resulted in the discovery of novel antagonists which maintained RARγ potency but were greater than 500-fold selective versus RARα and RARβ. The potent and selective RARγ antagonist LY2955303 demonstrated good pharmacokinetic properties and was efficacious in the MIA model of osteoarthritis-like joint pain. This compound demonstrated an improved margin to RARα-mediated adverse effects.

  • Organizational Affiliation

    Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor alpha246Homo sapiensMutation(s): 0 
Gene Names: RARANR1B1
UniProt & NIH Common Fund Data Resources
Find proteins for P10276 (Homo sapiens)
Explore P10276 
Go to UniProtKB:  P10276
GTEx:  ENSG00000131759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10276
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6Q7

Download Ideal Coordinates CCD File 
B [auth A]4-{5-(3-tert-butylphenyl)-1-[4-(methylsulfonyl)phenyl]-1H-pyrazol-3-yl}benzoic acid
C27 H26 N2 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
6Q7 BindingDB:  5K13 Ki: 1.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.496α = 90
b = 62.541β = 106.05
c = 49.347γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description