Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35286.10 
• Atom Count: 2416 
• Residue Count: 296 
• Unique protein chains: 1

4YTI

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

• DOI: 10.2210/pdb4YTI/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2015-03-17 Released: 2015-08-12 
• Deposition Author(s): Zuccola, H.J., Ledeboer, M.

---

Experimental Data Snapshot

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

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

• PubMed: 26230873 
• DOI: 10.1021/acs.jmedchem.5b00301
• Primary Citation of Related Structures:  
  4YTH, 4YTF, 4YTC


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tyrosine-protein kinase JAK2	A	296	Homo sapiens	Mutation(s): 0  Gene Names: JAK2 EC: 2.7.10.2
Find proteins for O60674 (Homo sapiens) Go to Gene View: JAK2 Go to UniProtKB:  O60674

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
VJK	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 Decernotinib, Adelatinib, VX-509 C18 H19 F3 N6 O ASUGUQWIHMTFJL-QGZVFWFLSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
VJK	IC50: 13 - 16400 nM (100) BINDINGDB
VJK	Ki: 13 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.217 
• R-Value Work: 0.207 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 94.932	α = 90.00
b = 100.981	β = 90.00
c = 68.407	γ = 90.00

Software Package:

Software Name	Purpose
BUSTER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-17 
• Released Date: 2015-08-12 
• Deposition Author(s): Zuccola, H.J., Ledeboer, M.

Revision History 

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