1ILH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORPHAN NUCLEAR RECEPTOR PXRA316Homo sapiensMutation(s): 0 
Gene Names: PXRNR1I2
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
NIH Common Fund Data Resources
PHAROS:  O75469
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRL
Query on SRL

Download Ideal Coordinates CCD File 
B [auth A][2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC ACID DIETHLYL ESTER
C24 H42 O7 P2
YQLJDECYQDRSBI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SRLEC50:  80   nM  BindingDB
SRLKd :  41   nM  PDBBind
SRLEC50:  440   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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