6Q7A | pdb_00006q7a

RORCVAR2 (RORGT, 264-499) IN COMPLEX WITH COMPOUND 4 AT 2.2A: Identification of N-aryl imidazoles as potent and selective RORgt inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.251 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 28.01 kDa 
  • Atom Count: 1,977 
  • Modeled Residue Count: 228 
  • Deposited Residue Count: 238 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HKZ
(Subject of Investigation/LOI)

Query on HKZ



Download:Ideal Coordinates CCD File
B [auth A]1-[2,6-bis(chloranyl)phenyl]-2-(furan-2-yl)-5-methyl-4-(phenylmethyl)imidazole
C21 H16 Cl2 N2 O
YQPVLABIYDUDBN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.251 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.201α = 90
b = 102.201β = 90
c = 129.582γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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