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

  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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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: https://doi.org/10.1021/bi0268753
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orphan Nuclear Receptor PXR316Homo sapiensMutation(s): 0 
Gene Names: NR1I2 or PXR
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
Query on HYF

Download Ideal Coordinates CCD File 
C35 H52 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
HYF PDBBind:  1M13 Kd: 27 (nM) from 1 assay(s)
Binding MOAD:  1M13 Kd: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.372α = 90
b = 91.372β = 90
c = 85.645γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations