5X0R

Crystal Structure of PXR LBD Complexed with SJB7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.665 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

SPA70 is a potent antagonist of human pregnane X receptor.

Lin, W.Wang, Y.M.Chai, S.C.Lv, L.Zheng, J.Wu, J.Zhang, Q.Wang, Y.D.Griffin, P.R.Chen, T.

(2017) Nat Commun 8: 741-741

  • DOI: 10.1038/s41467-017-00780-5

  • PubMed Abstract: 
  • Many drugs bind to and activate human pregnane X receptor (hPXR) to upregulate drug-metabolizing enzymes, resulting in decreased drug efficacy and increased resistance. This suggests that hPXR antagonists have therapeutic value. Here we report that S ...

    Many drugs bind to and activate human pregnane X receptor (hPXR) to upregulate drug-metabolizing enzymes, resulting in decreased drug efficacy and increased resistance. This suggests that hPXR antagonists have therapeutic value. Here we report that SPA70 is a potent and selective hPXR antagonist. SPA70 inhibits hPXR in human hepatocytes and humanized mouse models and enhances the chemosensitivity of cancer cells, consistent with the role of hPXR in drug resistance. Unexpectedly, SJB7, a close analog of SPA70, is an hPXR agonist. X-ray crystallography reveals that SJB7 resides in the ligand-binding domain (LBD) of hPXR, interacting with the AF-2 helix to stabilize the LBD for coactivator binding. Differential hydrogen/deuterium exchange analysis demonstrates that SPA70 and SJB7 interact with the hPXR LBD. Docking studies suggest that the lack of the para-methoxy group in SPA70 compromises its interaction with the AF-2, thus explaining its antagonism. SPA70 is an hPXR antagonist and promising therapeutic tool.The xenobiotic-activated human pregnane X receptor (hPXR) regulates drug metabolism. Here the authors develop hPXR modulators, which are of potential therapeutic interest and functionally and structurally characterize the antagonist SPA70 and the structurally related agonist SJB7.


    Organizational Affiliation

    Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA. taosheng.chen@stjude.org.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA.,Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA.,Structure Biology, Shanghai Medicilon Inc., Shanghai, 201299, China.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 1 group I member 2
A, B
316Homo sapiensMutation(s): 0 
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
C, D
25Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4WH
Query on 4WH

Download SDF File 
Download CCD File 
A, B
4-[(4-tert-butylphenyl)sulfonyl]-1-(2,4-dimethoxy-5-methylphenyl)-5-methyl-1H-1,2,3-triazole
C22 H27 N3 O4 S
HXRSXIPYPZGCEK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.665 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.339α = 90.00
b = 89.301β = 90.00
c = 106.759γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references