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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 79.46 kDa 
• Atom Count: 4896 
• Modelled Residue Count: 569 
• Deposited Residue Count: 688 
• Unique protein chains: 1

6P2B

Tethered PXR-LBD/SRC-1p bound to Garcinoic Acid

• PDB DOI: 10.2210/pdb6P2B/pdb

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


• Deposited: 2019-05-21 Released: 2020-04-01 
• Deposition Author(s): Walton, W.G., Pellock, S.J., Redinbo, M.R.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Garcinoic Acid Is a Natural and Selective Agonist of Pregnane X Receptor.

Bartolini, D., De Franco, F., Torquato, P., Marinelli, R., Cerra, B., Ronchetti, R., Schon, A., Fallarino, F., De Luca, A., Bellezza, G., Ferri, I., Sidoni, A., Walton, W.G., Pellock, S.J., Redinbo, M.R., Mani, S., Pellicciari, R., Gioiello, A., Galli, F.

(2020) J Med Chem 63: 3701-3712

• PubMed: 32160459 
• DOI: 10.1021/acs.jmedchem.0c00012
• Primary Citation of Related Structures:  
  6P2B


• PubMed Abstract: 
  

Pregnane X receptor (PXR) is a master xenobiotic-sensing transcription factor and a validated target for immune and inflammatory diseases. The identification of chemical probes to investigate the therapeutic relevance of the receptor is still highly desired. In fact, currently available PXR ligands are not highly selective and can exhibit toxicity and/or potential off-target effects. In this study, we have identified garcinoic acid as a selective and efficient PXR agonist. The properties of this natural molecule as a specific PXR agonist were demonstrated by the screening on a panel of nuclear receptors, the assessment of the physical and thermodynamic binding affinity, and the determination of the PXR-garcinoic acid complex crystal structure. Cytotoxicity, transcriptional, and functional properties were investigated in human liver cells, and compound activity and target engagement were confirmed in vivo in mouse liver and gut tissue. In conclusion, garcinoic acid is a selective natural agonist of PXR and a promising lead compound toward the development of new PXR-regulating modulators.

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Organizational Affiliation: 

Department of Pharmaceutical Sciences, University of Perugia, Perugia 06122, Italy.

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NQD (Subject of Investigation/LOI)	C [auth A], E [auth B]	(2Z,6E,10E)-13-[(2R)-6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2,6,10-trimethyltrideca-2,6,10-trienoic acid C27 H38 O4 QOFWRHWADNWKSU-HGPKLCRWSA-N
DMS	D [auth A], F [auth B], G [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.992	α = 90
b = 89.547	β = 90
c = 107.531	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-05-21 
• Released Date: 2020-04-01 
Deposition Author(s): Walton, W.G., Pellock, S.J., Redinbo, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	CA222469

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2020-04-22
  Changes: Database references