Crystal Structure of JAK2 complexed with a potent quinoxaline ATP site inhibitor

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Potent and Selective Inhibition of Polycythemia by the Quinoxaline JAK2 Inhibitor NVP-BSK805

Baffert, F.Regnier, C.H.De Pover, A.Pissot-Soldermann, C.Tavares, G.A.Blasco, F.Brueggen, J.Chene, P.Drueckes, P.Erdmann, D.Furet, P.Gerspacher, M.Lang, M.Ledieu, D.Nolan, L.Ruetz, S.Trappe, J.Vangrevelinghe, E.Wartmann, M.Wyder, L.Hofmann, F.Radimerski, T.

(2010) Mol Cancer Ther 9: 1945-1955

  • DOI: https://doi.org/10.1158/1535-7163.MCT-10-0053
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The recent discovery of an acquired activating point mutation in JAK2, substituting valine at amino acid position 617 for phenylalanine, has greatly improved our understanding of the molecular mechanism underlying chronic myeloproliferative neoplasms. Strikingly, the JAK2(V617F) mutation is found in nearly all patients suffering from polycythemia vera and in roughly every second patient suffering from essential thrombocythemia and primary myelofibrosis. Thus, JAK2 represents a promising target for the treatment of myeloproliferative neoplasms and considerable efforts are ongoing to discover and develop inhibitors of the kinase. Here, we report potent inhibition of JAK2(V617F) and JAK2 wild-type enzymes by a novel substituted quinoxaline, NVP-BSK805, which acts in an ATP-competitive manner. Within the JAK family, NVP-BSK805 displays more than 20-fold selectivity towards JAK2 in vitro, as well as excellent selectivity in broader kinase profiling. The compound blunts constitutive STAT5 phosphorylation in JAK2(V617F)-bearing cells, with concomitant suppression of cell proliferation and induction of apoptosis. In vivo, NVP-BSK805 exhibited good oral bioavailability and a long half-life. The inhibitor was efficacious in suppressing leukemic cell spreading and splenomegaly in a Ba/F3 JAK2(V617F) cell-driven mouse mechanistic model. Furthermore, NVP-BSK805 potently suppressed recombinant human erythropoietin-induced polycythemia and extramedullary erythropoiesis in mice and rats.

  • Organizational Affiliation

    Disease Area Oncology, Novartis Institutes for BioMedical Research, 4057 Basel, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2295Homo sapiensMutation(s): 0 
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 DQX

Download Ideal Coordinates CCD File 
B [auth A]8-[3,5-difluoro-4-(morpholin-4-ylmethyl)phenyl]-2-(1-piperidin-4-yl-1H-pyrazol-4-yl)quinoxaline
C27 H28 F2 N6 O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
DQX BindingDB:  3KRR Kd: 4.20e+4 (nM) from 1 assay(s)
IC50: 7.3 (nM) from 1 assay(s)
PDBBind:  3KRR IC50: 0.48 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.312α = 90
b = 103.009β = 90
c = 68.739γ = 90
Software Package:
Software NamePurpose
CCP4model building
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance