5W4R | pdb_00005w4r

Structure of RORgt bound to a tertiary alcohol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.245 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

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Ligand Structure Quality Assessment 


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Literature

6-Substituted quinolines as ROR gamma t inverse agonists.

Barbay, J.K., Cummings, M.D., Abad, M., Castro, G., Kreutter, K.D., Kummer, D.A., Maharoof, U., Milligan, C., Nishimura, R., Pierce, J., Schalk-Hihi, C., Spurlino, J., Tanis, V.M., Urbanski, M., Venkatesan, H., Wang, A., Woods, C., Wolin, R., Xue, X., Edwards, J.P., Fourie, A.M., Leonard, K.

(2017) Bioorg Med Chem Lett 27: 5277-5283

  • DOI: https://doi.org/10.1016/j.bmcl.2017.10.027
  • Primary Citation Related Structures: 
    5W4R, 5W4V

  • PubMed Abstract: 

    We identified 6-substituted quinolines as modulators of the retinoic acid receptor-related orphan receptor gamma t (RORγt). The synthesis of this class of RORγt modulators is reported, and optimization of the substituents at the quinoline 6-position that produced compounds with high affinity for the receptor is detailed. This effort identified molecules that act as potent, full inverse agonists in a RORγt-driven cell-based reporter assay. The X-ray crystal structures of two full inverse agonists from this chemical series bound to the RORγt ligand binding domain are disclosed, and we highlight the interaction of a hydrogen-bond acceptor on the 6-position substituent of the inverse agonist with Glu379:NH as a conserved binding contact.

    • Organizational Affiliation: 
    • Discovery Immunology, Janssen Research and Development, LLC, Welsh and McKean Roads, Spring House, PA 19477, United States. Electronic address: kbarbay@its.jnj.com.

Macromolecule Content 

  • Total Structure Weight: 51.63 kDa 
  • Atom Count: 3,593 
  • Modeled Residue Count: 431 
  • Deposited Residue Count: 434 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
217Homo sapiensMutation(s): 0 
Gene Names: RORC, NR1F3, RORG, RZRG
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
9WD

Query on 9WD


Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]		1-{4-[(R)-(4-chloro-2-methoxy-3-{[4-(1H-pyrazol-1-yl)phenyl]methyl}quinolin-6-yl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]piperidin-1-yl}ethan-1-one
C32 H33 Cl N6 O3
MAJOOHMQVBMIGI-JGCGQSQUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.361α = 90
b = 97.361β = 90
c = 128.218γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2017-12-27 
    • Deposition Author(s): Spurlino, J.

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Advisory, Data collection, Database references