7N2A | pdb_00007n2a

human PXR LBD bound to compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.255 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 07FClick on this verticalbar to view details

This is version 1.2 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: 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.


Macromolecules
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
07F (Subject of Investigation/LOI)
Query on 07F

Download Ideal Coordinates CCD File 
B [auth A]5-benzyl-2-(3-fluoro-2-hydroxyphenyl)-6-methyl-3-(2-phenylethyl)pyrimidin-4(3H)-one
C26 H23 F N2 O2
BFDADFMMNADXMI-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
07F BindingDB:  7N2A EC50: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.512α = 90
b = 91.512β = 90
c = 85.05γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 07FClick on this verticalbar to view details

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