6BNS

STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND TETHERED WITH SRC co-activator peptide and Compound 25a AKA BICYCLIC HEXAFLUOROISOPROPYL 2 ALCOHOL SULFONAMIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of bicyclic hexafluoroisopropyl alcohol sulfonamides as retinoic acid receptor-related orphan receptor gamma (ROR gamma /RORc) inverse agonists. Employing structure-based drug design to improve pregnane X receptor (PXR) selectivity.

Gong, H.Weinstein, D.S.Lu, Z.Duan, J.J.Stachura, S.Haque, L.Karmakar, A.Hemagiri, H.Raut, D.K.Gupta, A.K.Khan, J.Camac, D.Sack, J.S.Pudzianowski, A.Wu, D.R.Yarde, M.Shen, D.R.Borowski, V.Xie, J.H.Sun, H.D'Arienzo, C.Dabros, M.Galella, M.A.Wang, F.Weigelt, C.A.Zhao, Q.Foster, W.Somerville, J.E.Salter-Cid, L.M.Barrish, J.C.Carter, P.H.Dhar, T.G.M.

(2018) Bioorg Med Chem Lett 28: 85-93

  • DOI: 10.1016/j.bmcl.2017.12.006
  • Primary Citation of Related Structures:  
    6BN6, 6BNS

  • PubMed Abstract: 
  • We disclose the optimization of a high throughput screening hit to yield benzothiazine and tetrahydroquinoline sulfonamides as potent RORγt inverse agonists. However, a majority of these compounds showed potent activity against pregnane X receptor (PXR) and modest activity against liver X receptor α (LXRα) ...

    We disclose the optimization of a high throughput screening hit to yield benzothiazine and tetrahydroquinoline sulfonamides as potent RORγt inverse agonists. However, a majority of these compounds showed potent activity against pregnane X receptor (PXR) and modest activity against liver X receptor α (LXRα). Structure-based drug design (SBDD) led to the identification of benzothiazine and tetrahydroquinoline sulfonamide analogs which completely dialed out LXRα activity and were less potent at PXR. Pharmacodynamic (PD) data for compound 35 in an IL-23 induced IL-17 mouse model is discussed along with the implications of a high Y max in the PXR assay for long term preclinical pharmacokinetic (PK) studies.


    Organizational Affiliation

    Bristol-Myers Squibb, Research and Development, Princeton, NJ 08543-4000, United States. Electronic address: murali.dhar@bms.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 ChimeraA, B351Homo sapiensMutation(s): 0 
Gene Names: NR1I2PXRNCOA1BHLHE74SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
GTEx:  ENSG00000144852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO75469Q15788
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XGH
Query on XGH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-[(2S)-4-[(4-fluorophenyl)sulfonyl]-7-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-(2-hydroxy-2-methylpropyl)acetamide
C23 H23 F7 N2 O5 S2
XUCORPNQMQOUMD-HNNXBMFYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
XGH BindingDB:  6BNS EC50: min: 144, max: 175 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.37α = 90
b = 89.234β = 90
c = 105.902γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2018-01-03
    Changes: Database references