4XHD

STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN WITH COMPOUND-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Developing Adnectins That Target SRC Co-Activator Binding to PXR: A Structural Approach toward Understanding Promiscuity of PXR.

Khan, J.A., Camac, D.M., Low, S., Tebben, A.J., Wensel, D.L., Wright, M.C., Su, J., Jenny, V., Gupta, R.D., Ruzanov, M., Russo, K.A., Bell, A., An, Y., Bryson, J.W., Gao, M., Gambhire, P., Baldwin, E.T., Gardner, D., Cavallaro, C.L., Duncia, J.V., Hynes, J.

(2015) J.Mol.Biol. 427: 924-942

  • DOI: 10.1016/j.jmb.2014.12.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The human pregnane X receptor (PXR) is a promiscuous nuclear receptor that functions as a sensor to a wide variety of xenobiotics and regulates expression of several drug metabolizing enzymes and transporters. We have generated "Adnectins", derived f ...

    The human pregnane X receptor (PXR) is a promiscuous nuclear receptor that functions as a sensor to a wide variety of xenobiotics and regulates expression of several drug metabolizing enzymes and transporters. We have generated "Adnectins", derived from 10th fibronectin type III domain ((10)Fn3), that target the PXR ligand binding domain (LBD) interactions with the steroid receptor co-activator-1 (SRC-1) peptide, displacing SRC-1 binding. Adnectins are structurally homologous to the immunoglobulin superfamily. Three different co-crystal structures of PXR LBD with Adnectin-1 and CCR1 (CC chemokine receptor-1) antagonist Compound-1 were determined. This structural information was used to modulate PXR affinity for a related CCR1 antagonist compound that entered into clinical trials for rheumatoid arthritis. The structures of PXR with Adnectin-1 reveal specificity of Adnectin-1 in not only targeting the interface of the SRC-1 interactions but also engaging the same set of residues that are involved in binding of SRC-1 to PXR. Substituting SRC-1 with Adnectin-1 does not alter the binding conformation of Compound-1 in the ligand binding pocket. The structure also reveals the possibility of using Adnectins as crystallization chaperones to generate structures of PXR with compounds of interest.

    Related Citations: 
    • The discovery of BMS-457, a potent and selective CCR1 antagonist.
      Gardner, D.S.,Santella, J.B.,Duncia, J.V.,Carter, P.H.,Dhar, T.G.,Wu, H.,Guo, W.,Cavallaro, C.,Van Kirk, K.,Yarde, M.,Briceno, S.W.,Grafstrom, R.R.,Liu, R.,Patel, S.R.,Tebben, A.J.,Camac, D.,Khan, J.,Watson, A.,Yang, G.,Rose, A.,Foster, W.R.,Cvijic, M.E.,Davies, P.,Hynes, J.
      (2013) Bioorg.Med.Chem.Lett. 23: 3833

    Organizational Affiliation: 

    Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA. Electronic address: javed.khan@bms.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 1 group I member 2
A
315Homo sapiensMutation(s): 0 
Gene Names: NR1I2 (PXR)
Find proteins for O75469 (Homo sapiens)
Go to Gene View: NR1I2
Go to UniProtKB:  O75469
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
40U
Query on 40U
Download SDF File 
Download CCD File 
A
N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-2-cyclopropylacetamide
C23 H33 Cl N2 O3
CZEQXLMAKRKHJC-OFNKIYASSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.476α = 90.00
b = 91.476β = 90.00
c = 85.564γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2015-09-30
    Type: Database references