6Q6M

RORCVAR2 (RORGT, 264-499) IN COMPLEX WITH COMPOUND 1: Identification of N-aryl imidazoles as potent and selective RORgt inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HJWClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure-Based and Property-Driven Optimization ofN-Aryl Imidazoles toward Potent and Selective Oral ROR gamma t Inhibitors.

Hoegenauer, K.Kallen, J.Jimenez-Nunez, E.Strang, R.Ertl, P.Cooke, N.G.Hintermann, S.Voegtle, M.Betschart, C.McKay, D.J.J.Wagner, J.Ottl, J.Beerli, C.Billich, A.Dawson, J.Kaupmann, K.Streiff, M.Gobeau, N.Harlfinger, S.Stringer, R.Guntermann, C.

(2019) J Med Chem 62: 10816-10832

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01291
  • Primary Citation of Related Structures:  
    6Q6M, 6Q6O, 6Q7A, 6Q7H

  • PubMed Abstract: 

    Retinoic acid receptor-related orphan receptor gamma-t (RORγt) is considered to be the master transcription factor for the development of Th17 cells that produce proinflammatory cytokines such as IL-17A. Overproportionate Th17 cell abundance is associated with the pathogenesis of many inflammatory conditions including psoriasis. In a high-throughput fluorescence resonance energy transfer (FRET) screen, we identified compound 1 as a hit with promising lipophilic efficiency (LipE). Using structure-based drug design based on a number of X-ray cocrystal structures, we morphed this hit class into potent imidazoles, exemplified by compound 3 . To improve the poor absorption, distribution, metabolism, and excretion (ADME) properties of neutral imidazoles, we extended our ligands with carboxylic acid substituents toward a polar, water-rich area of the protein. This highly lipophilicity-efficient modification ultimately led to the discovery of compound 14 , a potent and selective inhibitor of RORγt with good ADME properties and excellent in vivo pharmacokinetics. This compound showed good efficacy in an in vivo delayed-type hypersensitivity pharmacology model in rats.


  • Organizational Affiliation

    Global Discovery Chemistry , 181 Massachusetts Avenue , 02139 Cambridge , Massachusetts , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma238Homo 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
GTEx:  ENSG00000143365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HJW (Subject of Investigation/LOI)
Query on HJW

Download Ideal Coordinates CCD File 
B [auth A]ethyl (2~{S})-2-[(2-chloranyl-6-methyl-phenyl)-thiophen-2-ylcarbonyl-amino]propanoate
C17 H18 Cl N O3 S
XYAGVCFCNDDPMS-LBPRGKRZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
HJW BindingDB:  6Q6M IC50: 128 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.015α = 90
b = 102.015β = 90
c = 128.86γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HJWClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2019-11-27 
  • Deposition Author(s): Kallen, J.

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description