5NU1

Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural States of ROR gamma t: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds.

Kallen, J.Izaac, A.Be, C.Arista, L.Orain, D.Kaupmann, K.Guntermann, C.Hoegenauer, K.Hintermann, S.

(2017) ChemMedChem 12: 1014-1021

  • DOI: 10.1002/cmdc.201700278
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The T-cell-specific retinoic acid receptor (RAR)-related orphan receptor-γ (RORγt) is a key transcription factor for the production of pro-inflammatory Th17 cytokines, which are implicated in the pathogenesis of autoimmune diseases. Over the years, s ...

    The T-cell-specific retinoic acid receptor (RAR)-related orphan receptor-γ (RORγt) is a key transcription factor for the production of pro-inflammatory Th17 cytokines, which are implicated in the pathogenesis of autoimmune diseases. Over the years, several structurally diverse RORγt inverse agonists have been reported, but combining high potency and good physicochemical properties has remained a challenging task. We recently reported a new series of inverse agonists based on an imidazopyridine core with good physicochemical properties and excellent selectivity. Herein we report eight new X-ray crystal structures for different classes of natural and synthetic compounds, including examples selected from the patent literature. Analysis of their respective binding modes revealed insight into the molecular mechanisms that lead to agonism, antagonism, or inverse agonism. We report new molecular mechanisms for RORγt agonism and propose a separation of the inverse agonists into two classes: those that act via steric clash and those that act via other mechanisms (for the latter, co-crystallization with a co-activator peptide and helix 12 in the agonist position is still possible). For the non-steric clash inverse agonists, we propose a new mechanism ("water trapping") which can be combined with other mechanisms (e.g., close contacts with H479). In addition, we compare the interactions made for selected compounds in the "back pocket" near S404 and in the "sulfate pocket" near R364 and R367. Taken together, these new mechanistic insights should prove useful for the design and optimization of further RORγt modulators.


    Organizational Affiliation

    CBT, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor ROR-gamma
A, B
257Homo sapiensMutation(s): 1 
Gene Names: RORC (NR1F3, RORG, RZRG)
Find proteins for P51449 (Homo sapiens)
Go to Gene View: RORC
Go to UniProtKB:  P51449
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor-interacting protein 1
P, Q
20Homo sapiensMutation(s): 0 
Gene Names: NRIP1
Find proteins for P48552 (Homo sapiens)
Go to Gene View: NRIP1
Go to UniProtKB:  P48552
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8YB
Query on 8YB

Download SDF File 
Download CCD File 
A, B
~{N}-[4-(3-chlorophenyl)-5-(2-chlorophenyl)carbonyl-1,3-thiazol-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide
C26 H20 Cl2 N2 O4 S2
GRWNPFJXINLSNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.389α = 90.00
b = 68.802β = 102.92
c = 82.866γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-28 
  • Released Date: 2017-06-21 
  • Deposition Author(s): Kallen, J.

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2018-10-03
    Type: Data collection