1M13

Crystal Structure of the Human Pregane X Receptor Ligand Binding Domain in Complex with Hyperforin, a Constituent of St. John's Wort


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

2.1 A Crystal Structure of Human PXR in Complex with the St. John's Wort Compound Hyperforin

Watkins, R.E.Maglich, J.M.Moore, L.B.Wisely, G.B.Noble, S.M.Davis-Searles, P.R.Lambert, M.H.Kliewer, S.A.Redinbo, M.R.

(2003) Biochemistry 42: 1430-1438

  • DOI: 10.1021/bi0268753

  • PubMed Abstract: 
  • The nuclear xenobiotic receptor PXR is activated by a wide variety of clinically used drugs and serves as a master regulator of drug metabolism and excretion gene expression in mammals. St. John's wort is used widely in Europe and the United States t ...

    The nuclear xenobiotic receptor PXR is activated by a wide variety of clinically used drugs and serves as a master regulator of drug metabolism and excretion gene expression in mammals. St. John's wort is used widely in Europe and the United States to treat depression. This unregulated herbal remedy leads to dangerous drug-drug interactions, however, in patients taking oral contraceptives, antivirals, or immunosuppressants. Such interactions are caused by the activation of the human PXR by hyperforin, the psychoactive agent in St. John's wort. In this study, we show that hyperforin induces the expression of numerous drug metabolism and excretion genes in primary human hepatocytes. We present the 2.1 A crystal structure of hyperforin in complex with the ligand binding domain of human PXR. Hyperforin induces conformational changes in PXR's ligand binding pocket relative to structures of human PXR elucidated previously and increases the size of the pocket by 250 A(3). We find that the mutation of individual aromatic residues within the ligand binding cavity changes PXR's response to particular ligands. Taken together, these results demonstrate that PXR employs structural flexibility to expand the chemical space it samples and that the mutation of specific residues within the ligand binding pocket of PXR tunes the receptor's response to ligands.


    Organizational Affiliation

    Department of Chemistry, The University of North Carolina at Chapel Hill, North Carolina 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orphan Nuclear Receptor PXR
A
316Homo sapiensGene 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
HYF
Query on HYF

Download SDF File 
Download CCD File 
A
4-HYDROXY-5-ISOBUTYRYL-6-METHYL-1,3,7-TRIS-(3-METHYL-BUT-2-ENYL)-6-(4-METHYL-PENT-3-ENYL)-BICYCLO[3.3.1]NON-3-ENE-2,9-DIONE
HYPERFORIN
C35 H52 O4
IWBJJCOKGLUQIZ-OJCNYLSASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HYFKd: 27 nM BINDINGMOAD
HYFKd: 27 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.372α = 90.00
b = 91.372β = 90.00
c = 85.645γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance