6S41

CRYSTAL STRUCTURE OF PXR IN COMPLEX WITH XPC-7455


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of CNS-Penetrant Aryl Sulfonamides as Isoform-Selective NaV1.6 Inhibitors with Efficacy in Mouse Models of Epilepsy.

Focken, T.Burford, K.Grimwood, M.E.Zenova, A.Andrez, J.C.Gong, W.Wilson, M.Taron, M.Decker, S.Lofstrand, V.Chowdhury, S.Shuart, N.Lin, S.Goodchild, S.J.Young, C.Soriano, M.Tari, P.K.Waldbrook, M.Nelkenbrecher, K.Kwan, R.Lindgren, A.de Boer, G.Lee, S.Sojo, L.DeVita, R.J.Cohen, C.J.Wesolowski, S.S.Johnson Jr., J.P.Dehnhardt, C.M.Empfield, J.R.

(2019) J Med Chem 62: 9618-9641

  • DOI: 10.1021/acs.jmedchem.9b01032
  • Primary Citation of Related Structures:  
    6S41

  • PubMed Abstract: 
  • Nonselective antagonists of voltage-gated sodium (Na V ) channels have been long used for the treatment of epilepsies. The efficacy of these drugs is thought to be due to the block of sodium channels on excitatory neurons, primarily Na V 1 ...

    Nonselective antagonists of voltage-gated sodium (Na V ) channels have been long used for the treatment of epilepsies. The efficacy of these drugs is thought to be due to the block of sodium channels on excitatory neurons, primarily Na V 1.6 and Na V 1.2. However, these currently marketed drugs require high drug exposure and suffer from narrow therapeutic indices. Selective inhibition of Na V 1.6, while sparing Na V 1.1, is anticipated to provide a more effective and better tolerated treatment for epilepsies. In addition, block of Na V 1.2 may complement the anticonvulsant activity of Na V 1.6 inhibition. We discovered a novel series of aryl sulfonamides as CNS-penetrant, isoform-selective Na V 1.6 inhibitors, which also displayed potent block of Na V 1.2. Optimization focused on increasing selectivity over Na V 1.1, improving metabolic stability, reducing active efflux, and addressing a pregnane X-receptor liability. We obtained compounds 30-32 , which produced potent anticonvulsant activity in mouse seizure models, including a direct current maximal electroshock seizure assay.


    Organizational Affiliation

    Xenon Pharmaceuticals Inc. , 200-3650 Gilmore Way , Burnaby , British Columbia V5G 4W8 , Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group I member 2A, B323Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KUB (Subject of Investigation/LOI)
Query on KUB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-[[(1~{S})-1-[2,5-bis(fluoranyl)phenyl]ethyl]amino]-5-chloranyl-2-fluoranyl-~{N}-(1,3-thiazol-4-yl)benzenesulfonamide
C17 H13 Cl F3 N3 O2 S2
KLWKJFRXLGLTIH-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.318α = 90
b = 89.002β = 90
c = 105.815γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.2: 2019-11-27
    Changes: Database references