2O9I

Crystal Structure of the Human Pregnane X Receptor LBD in complex with an SRC-1 coactivator peptide and T0901317


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the PXR-T1317 complex provides a scaffold to examine the potential for receptor antagonism.

Xue, Y.Chao, E.Zuercher, W.J.Willson, T.M.Collins, J.L.Redinbo, M.R.

(2007) Bioorg.Med.Chem. 15: 2156-2166

  • DOI: 10.1016/j.bmc.2006.12.026

  • PubMed Abstract: 
  • The human pregnane X receptor (PXR) recognizes a range of structurally and chemically distinct ligands and plays a key role in regulating the expression of protective gene products involved in the metabolism and excretion of potentially harmful compo ...

    The human pregnane X receptor (PXR) recognizes a range of structurally and chemically distinct ligands and plays a key role in regulating the expression of protective gene products involved in the metabolism and excretion of potentially harmful compounds. The identification and development of PXR antagonists is desirable as a potential way to control the up-regulation of drug metabolism pathways during the therapeutic treatment of disease. We present the 2.8A resolution crystal structure of the PXR ligand binding domain (LBD) in complex with T0901317 (T1317), which is also an agonist of another member of the orphan class of the nuclear receptor superfamily, the liver X receptor (LXR). In spite of differences in the size and shape of the receptors' ligand binding pockets, key interactions with this ligand are conserved between human PXR and human LXR. Based on the PXR-T1317 structure, analogues of T1317 were generated with the goal of designing an PXR antagonist effective via the receptor's ligand binding pocket. We find that selectivity in activating PXR versus LXR was achieved; such compounds may be useful in addressing neurodegenerative diseases like Niemann-Pick C. We were not successful, however, in producing a PXR antagonist. Based on these observations, we conclude that the generation of PXR antagonists targeted to the ligand binding pocket may be difficult due to the promiscuity and structural conformability of this xenobiotic sensor.


    Organizational Affiliation

    Department of Chemistry, CB#3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orphan nuclear receptor PXR
A, B
293Homo sapiensMutation(s): 1 
Gene Names: NR1I2 (PXR)
Find proteins for O75469 (Homo sapiens)
Go to Gene View: NR1I2
Go to UniProtKB:  O75469
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear Receptor Coactivator 1 isoform 3
C, D
15Mus musculusMutation(s): 0 
Gene Names: Ncoa1 (Src1)
EC: 2.3.1.48
Find proteins for P70365 (Mus musculus)
Go to UniProtKB:  P70365
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
444
Query on 444

Download SDF File 
Download CCD File 
A, B
N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE
C17 H12 F9 N O3 S
SGIWFELWJPNFDH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
444IC50: 40 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.979α = 90.00
b = 90.618β = 90.00
c = 105.725γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-12-13 
  • Released Date: 2007-01-30 
  • Deposition Author(s): Xue, Y., Redinbo, M.R.

Revision History 

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance