Discovery of VX-509 (Decernotinib): A Potent and Selective Janus kinase (JAK) 3 Inhibitor for the Treatment of Autoimmune Disease

Experimental Data Snapshot

  • Resolution: 2.52 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery of VX-509 (Decernotinib): A Potent and Selective Janus Kinase 3 Inhibitor for the Treatment of Autoimmune Diseases.

Farmer, L.J.Ledeboer, M.W.Hoock, T.Arnost, M.J.Bethiel, R.S.Bennani, Y.L.Black, J.J.Brummel, C.L.Chakilam, A.Dorsch, W.A.Fan, B.Cochran, J.E.Halas, S.Harrington, E.M.Hogan, J.K.Howe, D.Huang, H.Jacobs, D.H.Laitinen, L.M.Liao, S.Mahajan, S.Marone, V.Martinez-Botella, G.McCarthy, P.Messersmith, D.Namchuk, M.Oh, L.Penney, M.S.Pierce, A.C.Raybuck, S.A.Rugg, A.Salituro, F.G.Saxena, K.Shannon, D.Shlyakter, D.Swenson, L.Tian, S.K.Town, C.Wang, J.Wang, T.Wannamaker, M.W.Winquist, R.J.Zuccola, H.J.

(2015) J Med Chem 58: 7195-7216

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00301
  • Primary Citation of Related Structures:  
    4YTC, 4YTF, 4YTH, 4YTI

  • PubMed Abstract: 

    While several therapeutic options exist, the need for more effective, safe, and convenient treatment for a variety of autoimmune diseases persists. Targeting the Janus tyrosine kinases (JAKs), which play essential roles in cell signaling responses and can contribute to aberrant immune function associated with disease, has emerged as a novel and attractive approach for the development of new autoimmune disease therapies. We screened our compound library against JAK3, a key signaling kinase in immune cells, and identified multiple scaffolds showing good inhibitory activity for this kinase. A particular scaffold of interest, the 1H-pyrrolo[2,3-b]pyridine series (7-azaindoles), was selected for further optimization in part on the basis of binding affinity (Ki) as well as on the basis of cellular potency. Optimization of this chemical series led to the identification of VX-509 (decernotinib), a novel, potent, and selective JAK3 inhibitor, which demonstrates good efficacy in vivo in the rat host versus graft model (HvG). On the basis of these findings, it appears that VX-509 offers potential for the treatment of a variety of autoimmune diseases.

  • Organizational Affiliation

    Vertex Pharmaceuticals (Canada) Inc. , 275 Armand-Frappier, Laval, Québec H7V 4A7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2296Homo sapiensMutation(s): 0 
Gene Names: JAK2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
GTEx:  ENSG00000096968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60674
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on VJK

Download Ideal Coordinates CCD File 
B [auth A](2R)-2-methyl-2-[[2-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-N-[2,2,2-tris(fluoranyl)ethyl]butanamide
C18 H19 F3 N6 O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
VJK BindingDB:  4YTI Ki: 13 (nM) from 1 assay(s)
IC50: min: 13, max: 1.64e+4 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.52 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.932α = 90
b = 100.981β = 90
c = 68.407γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Other
  • Version 1.2: 2015-09-23
    Changes: Database references
  • Version 1.3: 2015-10-07
    Changes: Database references