5IXK

RORgamma in complex with inverse agonist BIO399.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.

Marcotte, D.J.Liu, Y.Little, K.Jones, J.H.Powell, N.A.Wildes, C.P.Silvian, L.F.Chodaparambil, J.V.

(2016) BMC Struct Biol 16: 7-7

  • DOI: https://doi.org/10.1186/s12900-016-0059-3
  • Primary Citation of Related Structures:  
    5IXK, 5IZ0

  • PubMed Abstract: 

    The nuclear hormone receptor RORγ regulates transcriptional genes involved in the production of the pro-inflammatory interleukin IL-17 which has been linked to autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. This transcriptional activity of RORγ is modulated through a protein-protein interaction involving the activation function 2 (AF2) helix on the ligand binding domain of RORγ and a conserved LXXLL helix motif on coactivator proteins. Our goal was to develop a RORγ specific inverse agonist that would help down regulate pro-inflammatory gene transcription by disrupting the protein protein interaction with coactivator proteins as a therapeutic agent.


  • Organizational Affiliation

    Chemical and Molecular Therapeutics, Biogen Inc, 250 Binney Street, Cambridge, MA, 02142, USA. doug.marcotte@biogenidec.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
228Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
PHAROS:  P51449
GTEx:  ENSG00000143365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6EW
Query on 6EW

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-(5-ethyl-3,3-dimethyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-8-yl)-3,4-dimethyl-N-(2,2,2-trifluoroethyl)benzene-1-sulfonamide
C23 H27 F3 N2 O4 S
NWOKNZFZDJIXMB-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6EW Binding MOAD:  5IXK IC50: 4.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.939α = 90
b = 56.167β = 124.77
c = 78.752γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data 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: 2016-06-15
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description