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 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 Binding MOAD:  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 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • 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 


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