4YTI

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

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

  • 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 an ...

    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 Inc. , 50 Northern Avenue, Boston, Massachusetts 02210, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2A296Homo sapiensMutation(s): 0 
Gene Names: JAK2
EC: 2.7.10.2
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
NIH Common Fund Data Resources
PHAROS  O60674
GTEx  ENSG00000096968
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VJK
Query on VJK
Download Ideal Coordinates CCD File 
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
ASUGUQWIHMTFJL-QGZVFWFLSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VJKIC50:  11200   nM  BindingDB
VJKIC50:  619   nM  BindingDB
VJKIC50:  10000   nM  BindingDB
VJKKi:  13   nM  BindingDB
VJKIC50:  24   nM  BindingDB
VJKIC50:  1870   nM  BindingDB
VJKIC50:  13   nM  BindingDB
VJKIC50:  130   nM  BindingDB
VJKIC50:  16400   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
BUSTERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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