2XA4

Inhibitors of Jak2 Kinase domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Discovery of 5-Chloro-N2-[(1S)-1-(5-Fluoropyrimidin-2-Yl) Ethyl]-N4-(5-Methyl-1H-Pyrazol-3-Yl)Pyrimidine-2,4-Diamine (Azd1480) as a Novel Inhibitor of the Jak/Stat Pathway

Ioannidis, S., Lamb, M.L., Wang, T., Almeida, L., Block, M.H., Davies, A.M., Peng, B., Su, M., Zhang, H., Hoffmann, E., Rivard, C., Green, I., Howard, T., Pollard, H., Read, J., Alimzhanov, M., Bebernitz, G., Bell, K., Ye, M., Huszar, D., Zinda, M.

(2011) J Med Chem 54: 262

  • DOI: https://doi.org/10.1021/jm1011319
  • Primary Citation of Related Structures:  
    2XA4

  • PubMed Abstract: 

    • The myeloproliferative neoplasms, polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis are a heterogeneous but related group of hematological malignancies characterized by clonal expansion of one or more myeloid lineages. The discovery of the Jak2 V617F gain of function mutation highlighted Jak2 as a potential therapeutic target in the MPNs ...

    The myeloproliferative neoplasms, polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis are a heterogeneous but related group of hematological malignancies characterized by clonal expansion of one or more myeloid lineages. The discovery of the Jak2 V617F gain of function mutation highlighted Jak2 as a potential therapeutic target in the MPNs. Herein, we disclose the discovery of a series of pyrazol-3-yl pyrimidin-4-amines and the identification of 9e (AZD1480) as a potent Jak2 inhibitor. 9e inhibits signaling and proliferation of Jak2 V617F cell lines in vitro, demonstrates in vivo efficacy in a TEL-Jak2 model, has excellent physical properties and preclinical pharmacokinetics, and is currently being evaluated in Phase I clinical trials.

    Organizational Affiliation: 

    Department of Cancer Chemistry, AstraZeneca R&D, Boston, Massachusetts, United States. stephanos.ioannidis@astrazeneca.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE JAK2A, B298Homo sapiensMutation(s): 2 
Gene Names: JAK2
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
PHAROS:  O60674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60674
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZ5
Query on AZ5
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		5-CHLORO-N2-[(1S)-1-(5-FLUOROPYRIMIDIN-2-YL)ETHYL]-N4-(5-METHYL-1H-PYRAZOL-3-YL)PYRIMIDINE-2,4-DIAMINE
C14 H14 Cl F N8
PDOQBOJDRPLBQU-QMMMGPOBSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A, B L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
AZ5 PDBBind:  2XA4 IC50: 3 (nM) from 1 assay(s)
BindingDB:  2XA4 IC50: 58 (nM) from 1 assay(s)
Binding MOAD:  2XA4 IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.854α = 90
b = 126.741β = 97.04
c = 134.342γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2015-04-01
    Changes: Database references
  • Version 1.3: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.4: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation