6DUP | pdb_00006dup

CRYSTAL STRUCTURE OF PXR IN COMPLEX WITH COMPOUND 7

• PDB DOI: https://doi.org/10.2210/pdb6DUP/pdb

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


• Deposited: 2018-06-21 Released: 2018-08-29 
• Deposition Author(s): Chen, X., Zhang, Y., Mclean, L.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.226 (Depositor), 0.225 (DCC) 

Literature

Amelioration of PXR-mediated CYP3A4 induction by mGluR2 modulators.

Vaz, R.J., Li, Y., Chellaraj, V., Reiling, S., Kuntzweiler, T., Yang, D., Shen, H., Batchelor, J.D., Zhang, Y., Chen, X., McLean, L.R., Kosley Jr., R.

(2018) Bioorg Med Chem Lett 28: 3194-3196

• PubMed: 30146095 
• DOI: https://doi.org/10.1016/j.bmcl.2018.08.022
• Primary Citation Related Structures: 
  6DUP


• PubMed Abstract: 
  

  This work describes the rational amelioration of Cytochrome P450 4/5 (CYP3A4/5) induction through the Pregnane-X Receptor (PXR) pathway in a series of compounds that modulate the metabotropic glutamate Receptor 2 (mGluR2) via an allosteric mechanism. The compounds were initially shown to induce CYP3A4/5 via the gold-standard induction assay measured in primary human hepatocytes. This was followed up by testing the compounds in a PXR assay which correlated well with the assay in primary cells. Further, one of the compounds was crystallized with PXR (pdb code 6DUP). Analysis of this co-crystal structure, together with previously published PXR co-crystal structures, lead to modification ideas. The compounds synthesized based on these ideas were shown not to be CYP3A4/5 inducers. The mGluR2 activity of the resulting compounds was maintained.

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Organizational Affiliation: 
• Integrated Drug Discovery, Sanofi US, 153-2nd Ave., Waltham, MA 02451, USA. Electronic address: [e-mail].
Integrated Drug Discovery, Sanofi US, 153-2nd Ave., Waltham, MA 02451, USA.
Pre-Development Sciences, Sanofi US, 153-2nd Ave., Waltham, MA 02451, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 78.76 kDa 
• Atom Count: 4,720 
• Modeled Residue Count: 562 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 1 group I member 2	A, B	344	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCJ	C [auth A]	(2S)-2-({[3'-(trifluoromethyl)[1,1'-biphenyl]-4-yl]oxy}methyl)-2,3-dihydro-7H-[1,3]oxazolo[3,2-a]pyrimidin-7-one C20 H15 F3 N2 O3 AYYWUDDPGRDIQB-KRWDZBQOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.226 (Depositor), 0.225 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.034	α = 90
b = 88.926	β = 90
c = 106.452	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Chen, X., Zhang, Y., Mclean, L.R.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2018-10-17
  Changes: Data collection, Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references