6XFV

CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C IN COMPLEX WITH A NOVEL INVERSE AGONIST

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Discovery of (3S,4S)-3-methyl-3-(4-fluorophenyl)-4-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxyprop-2-yl)phenyl)pyrrolidines as novel ROR gamma t inverse agonists.

Jiang, B., Duan, J.J., Stachura, S., Karmakar, A., Hemagiri, H., Raut, D.K., Gupta, A.K., Weigelt, C.A., Khan, J., Sack, J.S., Wu, D.R., Yarde, M., Shen, D.R., Galella, M.A., Mathur, A., Zhao, Q., Salter-Cid, L.M., Carter, P.H., Dhar, T.G.M.

(2020) Bioorg Med Chem Lett 30: 127392-127392

  • DOI: 10.1016/j.bmcl.2020.127392
  • Primary Citation of Related Structures:  
    6XFV

  • PubMed Abstract: 

    • A novel series of cis-3,4-diphenylpyrrolidines were designed as RORγt inverse agonists based on the binding conformation of previously reported bicyclic sulfonamide 1. Preliminary synthesis and structure-activity relationship (SAR) study established (3S,4S)-3-methyl-3-(4-fluorophenyl)-4-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxyprop-2-yl)phenyl)pyrrolidine as the most effective scaffold ...

    A novel series of cis-3,4-diphenylpyrrolidines were designed as RORγt inverse agonists based on the binding conformation of previously reported bicyclic sulfonamide 1. Preliminary synthesis and structure-activity relationship (SAR) study established (3S,4S)-3-methyl-3-(4-fluorophenyl)-4-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxyprop-2-yl)phenyl)pyrrolidine as the most effective scaffold. Subsequent SAR optimization led to identification of a piperidinyl carboxamide 31, which was potent against RORγt (EC 50 of 61 nM in an inverse agonist assay), selective relative to RORα, RORβ, LXRα and LXRβ, and stable in human and mouse liver microsomes. Furthermore, compound 31 exhibited considerably lower PXR Y max (46%) and emerged as a promising lead. The binding mode of the diphenylpyrrolidine series was established with an X-ray co-crystal structure of 10A/RORγt.

    Organizational Affiliation: 

    Research and Early Development, Bristol Myers Squibb Company, Princeton, NJ 08543-4000, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gammaA, B265Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V27 (Subject of Investigation/LOI)
Query on V27
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		1-(4-{(3S,4S)-4-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]-3-methyl-3-phenylpyrrolidine-1-carbonyl}piperidin-1-yl)ethan-1-one
C28 H30 F6 N2 O3
YXYVNJXYQMACDG-UKILVPOCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.867α = 90
b = 97.867β = 90
c = 130.355γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2020-06-16 
  • Released Date: 2020-08-12 
    • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release