6G05

RORGT (264-518;C455S) IN COMPLEX WITH INVERSE AGONIST "CPD-2" AND RIP140 PEPTIDE AT 1.90A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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

  • 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
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
GTEx:  ENSG00000143365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor-interacting protein 1C [auth P],
D [auth Q]
20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P48552 (Homo sapiens)
Explore P48552 
Go to UniProtKB:  P48552
GTEx:  ENSG00000180530 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48552
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EF5
Query on EF5

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
2-(4-ethylsulfonylphenyl)-~{N}-[4-phenyl-5-(phenylcarbonyl)-1,3-thiazol-2-yl]ethanamide
C26 H22 N2 O4 S2
MDMLFHGEDDZHNU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EF5 BindingDB:  6G05 IC50: min: 10, max: 316 (nM) from 7 assay(s)
EC50: 251 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.092α = 90
b = 70.079β = 101.58
c = 81.996γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • 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: 2024-01-17
    Changes: Data collection, Database references, Refinement description