6HJ2

Crystal structure of hPXR in complex with dabrafenib

  • Classification: NUCLEAR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2018-08-31 Released: 2020-03-25 
  • Deposition Author(s): Granell, M., Delfosse, V., Bourguet, W.
  • Funding Organization(s): French National Research Agency, National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-Based and Knowledge-Informed Design of B-Raf Inhibitors Devoid of Deleterious PXR Binding.

Schneider, M.Delfosse, V.Gelin, M.Grimaldi, M.Granell, M.Heriaud, L.Pons, J.L.Cohen Gonsaud, M.Balaguer, P.Bourguet, W.Labesse, G.

(2022) J Med Chem 65: 1552-1566

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01354
  • Primary Citation of Related Structures:  
    6HJ2, 7P3V

  • PubMed Abstract: 

    Dabrafenib is an anticancer drug currently used in the clinics, alone or in combination. However, dabrafenib was recently shown to potently activate the human nuclear receptor pregnane X receptor (PXR). PXR activation increases the clearance of various chemicals and drugs, including dabrafenib itself. It may also enhance cell proliferation and tumor aggressiveness. Therefore, there is a need for rational design of a potent protein kinase B-Raf inhibitor devoid of binding to the secondary target PXR and resisting rapid metabolism. By determining the crystal structure of dabrafenib bound to PXR and analyzing its mode of binding to both PXR and its primary target, B-Raf-V600E, we were able to derive new compounds with nanomolar activity against B-Raf and no detectable affinity for PXR. The crystal structure of B-Raf in complex with our lead compound revealed a subdomain swapping of the activation loop with potentially important functional implications for a prolonged inhibition of B-Raf-V600E.


  • Organizational Affiliation

    Centre de Biologie Structurale (CBS), CNRS, INSERM, Univ Montpellier, F-34090 Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group I member 2315Homo sapiensMutation(s): 0 
Gene Names: NR1I2PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
GTEx:  ENSG00000144852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75469
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
P06 BindingDB:  6HJ2 EC50: 87 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.39α = 90
b = 91.39β = 90
c = 85.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05
French National Research AgencyFranceANR-13-CESA-0017-03
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)FranceSYNERPXR2
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)FranceXenomix
National Institutes of Health/National Cancer Institute (NIH/NCI)FranceGSO-BRAFvsPXR

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-06-05
    Changes: Database references