5K13

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2016.05.056

  • 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 difference ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor alpha
A
246Homo sapiensMutation(s): 0 
Gene Names: RARA (NR1B1)
Find proteins for P10276 (Homo sapiens)
Go to Gene View: RARA
Go to UniProtKB:  P10276
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6Q7
Query on 6Q7

Download SDF File 
Download CCD File 
A
4-{5-(3-tert-butylphenyl)-1-[4-(methylsulfonyl)phenyl]-1H-pyrazol-3-yl}benzoic acid
C27 H26 N2 O4 S
HPXXLUZXJROKDE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.496α = 90.00
b = 62.541β = 106.05
c = 49.347γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-05-17 
  • Released Date: 2016-06-22 
  • Deposition Author(s): Wang, Y., Stout, S.L.

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release