5WIL

JAK2 Pseudokinase in complex with AZD7762


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and structural characterization of ATP-site ligands for the wild-type and V617F-mutant JAK2 pseudokinase domain.

McNally, R.Li, Q.Li, K.Dekker, C.Vangrevelinghe, E.Jones, M.Chene, P.Machauer, R.Radimerski, T.Eck, M.J.

(2019) ACS Chem. Biol. --: --

  • DOI: 10.1021/acschembio.8b00722
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The oncogenic V617F mutation lies in the pseudokinase domain of JAK2, marking it as a potential target for development of compounds that might inhibit the pathogenic activity of the mutant protein. We used differential scanning fluorimetry to identif ...

    The oncogenic V617F mutation lies in the pseudokinase domain of JAK2, marking it as a potential target for development of compounds that might inhibit the pathogenic activity of the mutant protein. We used differential scanning fluorimetry to identify compounds that bind the JAK2 pseudokinase domain. Crystal structures of five candidate compounds with the wild-type domain reveal their modes of binding. Exploration of analogs of screening hit BI-D1870 led to the identification of compound 2, a 123 nM ligand for the pseudokinase domain. Interestingly, crystal structures of the V617F domain in complex with two unrelated compounds reveal a conformation that is characteristic of the wild-type domain, rather than that previously observed for the V617F mutant. These structures suggest that certain ATP-site ligands can modulate the V617F allosteric site, thereby providing a mechanistic rationale for targeting the pseudokinase domain and a structural foundation for development of more potent and pseudokinase-selective compounds.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology , Dana-Farber Cancer Institute , Boston , Massachusetts 02115 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK2
A
277Homo sapiensMutation(s): 3 
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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YDJ
Query on YDJ

Download SDF File 
Download CCD File 
A
5-(3-fluorophenyl)-N-[(3S)-3-piperidyl]-3-ureido-thiophene-2-carboxamide
C17 H19 F N4 O2 S
IAYGCINLNONXHY-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.618α = 90.00
b = 60.674β = 90.00
c = 90.451γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2019-03-20
    Type: Data collection, Database references