7RIO

human PXR LBD bound to GSK003


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Overcoming the Pregnane X Receptor Liability: Rational Design to Eliminate PXR-Mediated CYP Induction.

Ramanjulu, J.M.Williams, S.P.Lakdawala, A.S.DeMartino, M.P.Lan, Y.Marquis, R.W.

(2021) ACS Med Chem Lett 12: 1396-1404

  • DOI: 10.1021/acsmedchemlett.1c00187
  • Primary Citation of Related Structures:  
    7N2A, 7RIO, 7RIU, 7RIV

  • PubMed Abstract: 
  • The pregnane X receptor (PXR) regulates expression of proteins responsible for all three phases required for the detoxification mechanism, which include CYP450 enzymes, phase II enzymes, and multidrug efflux pumps. Therefore, PXR is a prominent receptor that is responsible for xenobiotic excretion and drug-drug interactions ...

    The pregnane X receptor (PXR) regulates expression of proteins responsible for all three phases required for the detoxification mechanism, which include CYP450 enzymes, phase II enzymes, and multidrug efflux pumps. Therefore, PXR is a prominent receptor that is responsible for xenobiotic excretion and drug-drug interactions. Pyrimidinone 1 is an antagonist of the calcium sensing receptor (CaSR) and a strong activator of PXR. Repeat oral administration revealed diminished exposures over time, which prohibited further progression. A medicinal chemistry campaign was initiated to understand and abolish activation of PXR in order to increase systemic exposures. Rational structure-activity relationship investigations utilizing cocrystal structures and a de novo pharmacophore model resulted in compounds devoid of PXR activation. These studies culminated in the first orally active CaSR antagonist 8 suitable for progression. Cocrystallography, the pharmacophore model employed, and additional observations reported herein supported rational elimination of PXR activation and have applicability across diverse chemical classes to help erase PXR-driven drug-drug interactions.


    Organizational Affiliation

    GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 1C of Nuclear receptor subfamily 1 group I member 2A298Homo sapiensMutation(s): 0 
Gene Names: NR1I2PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75469
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5YX
Query on 5YX

Download Ideal Coordinates CCD File 
B [auth A]N-[3-(2-tert-butyl-5-{2-[2-(methanesulfonyl)ethyl]pyrimidin-4-yl}-1,3-thiazol-4-yl)-2-fluorophenyl]-2,5-difluorobenzene-1-sulfonamide
C26 H25 F3 N4 O4 S3
JZYMCONNLXIIJS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.392α = 90
b = 91.392β = 90
c = 85.211γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references