5IXK | pdb_00005ixk

RORgamma in complex with inverse agonist BIO399.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.263 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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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 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. We identified a novel series of synthetic benzoxazinone ligands having an agonist (BIO592) and inverse agonist (BIO399) mode of action in a FRET based assay. We show that the AF2 helix of RORγ is proteolytically sensitive when inverse agonist BIO399 binds. Using x-ray crystallography we show how small modifications on the benzoxazinone agonist BIO592 trigger inverse agonism of RORγ. Using an in vivo reporter assay, we show that the inverse agonist BIO399 displayed specificity for RORγ over ROR sub-family members α and β. The synthetic benzoxazinone ligands identified in our FRET assay have an agonist (BIO592) or inverse agonist (BIO399) effect by stabilizing or destabilizing the agonist conformation of RORγ. The proteolytic sensitivity of the AF2 helix of RORγ demonstrates that it destabilizes upon BIO399 inverse agonist binding perturbing the coactivator protein binding site. Our structural investigation of the BIO592 agonist and BIO399 inverse agonist structures identified residue Met358 on RORγ as the trigger for RORγ specific inverse agonism.


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

Macromolecule Content 

  • Total Structure Weight: 54.08 kDa 
  • Atom Count: 3,568 
  • Modeled Residue Count: 439 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.263 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
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