human PXR LBD bound to GSK001

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 1C of Nuclear receptor subfamily 1 group I member 2298Homo 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
GTEx:  ENSG00000144852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75469
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P06 (Subject of Investigation/LOI)
Query on P06

Download Ideal Coordinates CCD File 
B [auth A]Dabrafenib
C23 H20 F3 N5 O2 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.559α = 90
b = 91.559β = 90
c = 85.17γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
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
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description