4C61 | pdb_00004c61

Inhibitors of Jak2 Kinase domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.217 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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

Literature

Discovery of 1-Methyl-1H-Imidazole Derivatives as Potent Jak2 Inhibitors.

Su, Q., Ioannidis, S., Chuaqui, C., Almeida, L., Alimzhanov, M., Bebernitz, G., Bell, K., Block, M., Howard, T., Huang, S., Huszar, D., Read, J.A., Rivard Costa, C., Shi, J., Su, M., Ye, M., Zinda, M.

(2014) J Med Chem 57: 144

  • DOI: https://doi.org/10.1021/jm401546n
  • Primary Citation Related Structures: 
    4C61, 4C62

  • PubMed Abstract: 

    Structure based design, synthesis, and biological evaluation of a novel series of 1-methyl-1H-imidazole, as potent Jak2 inhibitors to modulate the Jak/STAT pathway, are described. Using the C-ring fragment from our first clinical candidate AZD1480 (24), optimization of the series led to the discovery of compound 19a, a potent, orally bioavailable Jak2 inhibitor. Compound 19a displayed a high level of cellular activity in hematopoietic cell lines harboring the V617F mutation and in murine BaF3 TEL-Jak2 cells. Compound 19a demonstrated significant tumor growth inhibition in a UKE-1 xenograft model within a well-tolerated dose range.

    • Organizational Affiliation: 
    • AstraZeneca, Oncology Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Macromolecule Content 

  • Total Structure Weight: 71.14 kDa 
  • Atom Count: 4,660 
  • Modeled Residue Count: 550 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE JAK2
A, B
298Homo sapiensMutation(s): 2 
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
PHAROS:  O60674
GTEx:  ENSG00000096968 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60674
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
LMM BindingDB:  4C61 IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.217 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.88α = 90
b = 127.09β = 97.33
c = 135.21γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALEPACKdata 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: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary