6G07

RORGT (264-518;C455S) IN COMPLEX WITH INVERSE AGONIST "CPD-9" AND RIP140 PEPTIDE AT 1.66A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Optimizing a Weakly Binding Fragment into a Potent ROR gamma t Inverse Agonist with Efficacy in an in Vivo Inflammation Model.

Carcache, D.A.Vulpetti, A.Kallen, J.Mattes, H.Orain, D.Stringer, R.Vangrevelinghe, E.Wolf, R.M.Kaupmann, K.Ottl, J.Dawson, J.Cooke, N.G.Hoegenauer, K.Billich, A.Wagner, J.Guntermann, C.Hintermann, S.

(2018) J Med Chem 61: 6724-6735

  • DOI: 10.1021/acs.jmedchem.8b00529
  • Primary Citation of Related Structures:  
    6G07, 6G05, 6FZU

  • PubMed Abstract: 
  • The transcription factor RORγt is an attractive drug-target due to its role in the differentiation of IL-17 producing Th17 cells that play a critical role in the etiopathology of several autoimmune diseases. Identification of starting points for RORγt inverse agonists with good properties has been a challenge ...

    The transcription factor RORγt is an attractive drug-target due to its role in the differentiation of IL-17 producing Th17 cells that play a critical role in the etiopathology of several autoimmune diseases. Identification of starting points for RORγt inverse agonists with good properties has been a challenge. We report the identification of a fragment hit and its conversion into a potent inverse agonist through fragment optimization, growing and merging efforts. Further analysis of the binding mode revealed that inverse agonism was achieved by an unusual mechanism. In contrast to other reported inverse agonists, there is no direct interaction or displacement of helix 12 observed in the crystal structure. Nevertheless, compound 9 proved to be efficacious in a delayed-type hypersensitivity (DTH) inflammation model in rats.


    Organizational Affiliation

    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaA, C [auth B], E [auth C], G [auth D]257Homo sapiensMutation(s): 1 
Gene Names: RORCNR1F3RORGRZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
PHAROS:  P51449
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor-interacting protein 1B [auth P], D [auth Q], F [auth R], H [auth S]20Homo sapiensMutation(s): 0 
Gene Names: NRIP1
UniProt & NIH Common Fund Data Resources
Find proteins for P48552 (Homo sapiens)
Explore P48552 
Go to UniProtKB:  P48552
PHAROS:  P48552
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EEZ
Query on EEZ

Download Ideal Coordinates CCD File 
I [auth A], J [auth B], K [auth C], L [auth D]~{N}-[5-chloranyl-6-[(1~{S})-1-phenylethoxy]pyridin-3-yl]-2-(4-ethylsulfonylphenyl)ethanamide
C23 H23 Cl N2 O4 S
VMHNMQCWPLURSW-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EEZKd:  35.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.935α = 90
b = 68.058β = 110.83
c = 96.522γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-03-16 
  • Released Date: 2018-07-18 
  • Deposition Author(s): Kallen, J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection