Crystal Structure of Human Pregnane X Receptor Ligand Binding Domain Bound to SR12813

Experimental Data Snapshot

  • Resolution: 2.76 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

Starting Model: experimental
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The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity.

Watkins, R.E.Wisely, G.B.Moore, L.B.Collins, J.L.Lambert, M.H.Williams, S.P.Willson, T.M.Kliewer, S.A.Redinbo, M.R.

(2001) Science 292: 2329-2333

  • DOI: https://doi.org/10.1126/science.1060762
  • Primary Citation of Related Structures:  
    1ILG, 1ILH

  • PubMed Abstract: 

    The human nuclear pregnane X receptor (hPXR) activates cytochrome P450-3A expression in response to a wide variety of xenobiotics and plays a critical role in mediating dangerous drug-drug interactions. We present the crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterol-lowering drug SR12813 at resolutions of 2.5 and 2.75 angstroms, respectively. The hydrophobic ligand-binding cavity of hPXR contains a small number of polar residues, permitting SR12813 to bind in three distinct orientations. The position and nature of these polar residues were found to be critical for establishing the precise pharmacologic activation profile of PXR. Our findings provide important insights into how hPXR detects xenobiotics and may prove useful in predicting and avoiding drug-drug interactions.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC 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: PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  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 SRL

Download Ideal Coordinates CCD File 
C24 H42 O7 P2
Binding Affinity Annotations 
IDSourceBinding Affinity
SRL PDBBind:  1ILH Kd: 41 (nM) from 1 assay(s)
BindingDB:  1ILH EC50: min: 60, max: 440 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.76 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.345α = 90
b = 91.345β = 90
c = 85.302γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description