Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.89 kDa 
• Atom Count: 4199 
• Modelled Residue Count: 524 
• Deposited Residue Count: 682 
• Unique protein chains: 2

5X0R

Crystal Structure of PXR LBD Complexed with SJB7

• PDB DOI: 10.2210/pdb5X0R/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-23 Released: 2017-10-04 
• Deposition Author(s): Lv, L., Lin, W., Chai, S.C., Zhang, Q., Chen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

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

• PubMed: 28963450 
• DOI: 10.1038/s41467-017-00780-5
• Primary Citation of Related Structures:  
  5X0R


• 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 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.

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Organizational Affiliation: 

Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 1 group I member 2	A, B	316	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2, PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens) Explore O75469  Go to UniProtKB:  O75469
PHAROS:  O75469 GTEx:  ENSG00000144852

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	C, D	25	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4WH	E [auth A], F [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
4WH	BindingDB:  5X0R	IC50: 340 (nM) from 1 assay(s)
		EC50: 880 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.339	α = 90
b = 89.301	β = 90
c = 106.759	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-01-23 
• Released Date: 2017-10-04 
Deposition Author(s): Lv, L., Lin, W., Chai, S.C., Zhang, Q., Chen, T.

Revision History  

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