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 6NX1 | pdb_00006nx1

STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND TETHERED WITH SRC CO-ACTIVATOR PEPTIDE AND COMPOUND-3 AKA 1,1,1,3,3,3-HEXAFLUORO-2-{4-[1-(4- LUOROBENZENESULFONYL)CYCLOPENTYL]PHENYL}PROPAN-2-OL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.240 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6NX1

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: 80.73 kDa 
  • Atom Count: 4,686 
  • Modeled Residue Count: 582 
  • Deposited Residue Count: 702 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 fusion
A, B
351Homo sapiensMutation(s): 0 
Gene Names: NR1I2, PXR, NCOA1, BHLHE74, SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
GTEx:  ENSG00000144852 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ15788O75469
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L7D

Query on L7D



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
1,1,1,3,3,3-hexafluoro-2-(4-{1-[(4-fluorophenyl)sulfonyl]cyclopentyl}phenyl)propan-2-ol
C20 H17 F7 O3 S
BANKSZZTXXTYRE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
L7D BindingDB:  6NX1 EC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.240 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.195α = 90
b = 89.612β = 90
c = 106.158γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-02-12 
  • Deposition Author(s): Khan, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references