3R8D

Activation of the Human Nuclear Xenobiotic Receptor PXR by the Reverse Transcriptase-Targeted Anti-HIV Drug PNU-142721


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Activation of the human nuclear xenobiotic receptor PXR by the reverse transcriptase-targeted anti-HIV drug PNU-142721.

Cheng, Y.Redinbo, M.R.

(2011) Protein Sci. 20: 1713-1719

  • DOI: 10.1002/pro.706

  • PubMed Abstract: 
  • The human pregnane X receptor (PXR) is a member of the nuclear receptor superfamily of ligand-regulated transcription factors. PXR responds to a structurally diverse variety of endogenous and xenobiotic compounds, and coordinates the expression of ge ...

    The human pregnane X receptor (PXR) is a member of the nuclear receptor superfamily of ligand-regulated transcription factors. PXR responds to a structurally diverse variety of endogenous and xenobiotic compounds, and coordinates the expression of genes central to the metabolism and excretion of potentially harmful chemicals, including human therapeutics. The reverse transcriptase inhibitor PNU-142721 has been designed to treat human immunodeficiency virus (HIV) infection. Although this compound has anti-HIV activity, it was established using cell-based assays that PNU-142721 is an efficacious PXR agonist. We present here the 2.8 Å resolution crystal structure of the human PXR ligand-binding domain in complex with PNU-142721. PXR employs one hydrogen bond and fourteen van der Waals contacts to interact with the ligand, but allows two loops adjacent to the ligand-binding pocket to remain disordered in the structure. These observations highlight the role structural flexibility plays in PXR's promiscuous responses to xenobiotics. The crystal structure also explains why PNU-173575, a thiomethyl metabolite of PNU-142721, exhibits enhanced PXR activation relative to the unmodified compound and why PNU-142721 can also activate rat PXR. Taken together, the results presented here elucidate the structural basis for PXR activation by PNU-142721 and related chemicals.


    Organizational Affiliation

    Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, North Carolina 27599-3290, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 1 group I member 2
A
316Homo sapiensMutation(s): 0 
Gene Names: NR1I2 (PXR)
Find proteins for O75469 (Homo sapiens)
Go to Gene View: NR1I2
Go to UniProtKB:  O75469
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNU
Query on PNU

Download SDF File 
Download CCD File 
A
6-CHLORO-2-(1-FURO[2,3-C]PYRIDIN-5-YL-ETHYLSULFANYL)-PYRIMIDIN-4-YLAMINE
C13 H11 Cl N4 O S
ATCRIOJPQXDFNY-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.238 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.284α = 90.00
b = 92.284β = 90.00
c = 84.380γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2011-10-05
    Type: Database references