6O98 | pdb_00006o98

Crystal structure of RAR-related orphan receptor C in complex with a phenyl (3-phenylpyrrolidin-3-yl)sulfone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.276 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-based Discovery of Phenyl (3-Phenylpyrrolidin-3-yl)sulfones as Selective, Orally Active ROR gamma t Inverse Agonists.

Duan, J.J.Lu, Z.Jiang, B.Stachura, S.Weigelt, C.A.Sack, J.S.Khan, J.Ruzanov, M.Galella, M.A.Wu, D.R.Yarde, M.Shen, D.R.Shuster, D.J.Borowski, V.Xie, J.H.Zhang, L.Vanteru, S.Gupta, A.K.Mathur, A.Zhao, Q.Foster, W.Salter-Cid, L.M.Carter, P.H.Dhar, T.G.M.

(2019) ACS Med Chem Lett 10: 367-373

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00010
  • Primary Citation Related Structures: 
    6NX1, 6O98

  • PubMed Abstract: 

    A new phenyl (3-phenylpyrrolidin-3-yl)sulfone series of RORγt inverse agonists was discovered utilizing the binding conformation of previously reported bicyclic sulfonamide 1 . Through a combination of structure-based design and structure-activity relationship studies, a polar set of amides at N 1-position of the pyrrolidine ring and perfluoroisopropyl group at para -position of the 3-phenyl group were identified as critical structural elements to achieve high selectivity against PXR, LXRα, and LXRβ. Further optimization led to the discovery of (1 R ,4r)-4-(( R )-3-((4-fluorophenyl)sulfonyl)-3-(4-(perfluoropropan-2-yl)phenyl)pyrrolidine-1-carbonyl)cyclohexane-1-carboxylic acid ( 26 ), which displayed excellent selectivity, desirable liability and pharmacokinetic properties in vitro , and a good pharmacokinetic profile in mouse. Oral administration of 26 demonstrated dose-dependent inhibition of IL-17 production in a mouse IL-2/IL-23-induced pharmacodynamic model and biologic-like efficacy in an IL-23-induced mouse acanthosis model.


  • Organizational Affiliation
    • Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08543-4000, United States.

Macromolecule Content 

  • Total Structure Weight: 62.67 kDa 
  • Atom Count: 3,705 
  • Modeled Residue Count: 446 
  • Deposited Residue Count: 530 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
265Homo sapiensMutation(s): 0 
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
L8A

Query on L8A



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
1-(4-{(3R)-3-[(4-fluorophenyl)sulfonyl]-3-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]pyrrolidine-1-carbonyl}piperazin-1-yl)ethan-1-one
C26 H26 F7 N3 O5 S
LGFLFKROQCMBLV-QHCPKHFHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
L8A BindingDB:  6O98 IC50: 44 (nM) from 1 assay(s)
EC50: 55 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.276 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.78α = 90
b = 97.78β = 90
c = 126.28γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2019-03-20 
  • Deposition Author(s): Sack, J.S.
  • This entry supersedes: 6NXH

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description