8R81 | pdb_00008r81

Crystal structure of the hPXR-LBD in complex with compound JMV6845

• PDB DOI: https://doi.org/10.2210/pdb8R81/pdb

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


• Deposited: 2023-11-27 Released: 2025-06-11 
• Deposition Author(s): Delfosse, V., Huet, T., Bourguet, W.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.221 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the hPXR-LBD in complex with compound JMV6845

Delfosse, V., Huet, T., Bourguet, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.31 kDa 
• Atom Count: 2,268 
• Modeled Residue Count: 273 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 1 group I member 2	A	320	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y8B (Subject of Investigation/LOI)	C [auth A]	2,4,6-trimethyl-~{N}-[1-(phenylmethyl)benzimidazol-5-yl]benzenesulfonamide C23 H23 N3 O2 S NZGPNMYYBHSCBR-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	B [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.221 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.849	α = 90
b = 90.849	β = 90
c = 86.682	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Delfosse, V., Huet, T., Bourguet, W.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-17-CE18-035

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release