5UT3

JAK2 JH2 in complex with IKK-2 Inhibitor VI

• PDB DOI: https://doi.org/10.2210/pdb5UT3/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-02-14 Released: 2017-06-07 
• Deposition Author(s): Puleo, D.E., Schlessinger, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Gilead Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.170 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

Identification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders.

Puleo, D.E., Kucera, K., Hammaren, H.M., Ungureanu, D., Newton, A.S., Silvennoinen, O., Jorgensen, W.L., Schlessinger, J.

(2017) ACS Med Chem Lett 8: 618-621

• PubMed: 28626521 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00153
• Primary Citation of Related Structures:  
  5USY, 5USZ, 5UT0, 5UT1, 5UT2, 5UT3


• PubMed Abstract: 
  

  Janus kinases (JAKs) regulate hematopoiesis via the cytokine-mediated JAK-STAT signaling pathway. JAKs contain tandem C-terminal pseudokinase (JH2) and tyrosine kinase (JH1) domains. The JAK2 pseudokinase domain adopts a protein kinase fold and, despite its pseudokinase designation, binds ATP with micromolar affinity. Recent evidence shows that displacing ATP from the JAK2 JH2 domain alters the hyperactivation state of the oncogenic JAK2 V617F protein while sparing the wild type JAK2 protein. In this study, small molecule binders of JAK2 JH2 were identified via an in vitro screen. Top hits were characterized using biophysical and structural approaches. Development of pseudokinase-selective compounds may offer novel pharmacological opportunities for treating cancers driven by JAK2 V617F and other oncogenic JAK mutants.

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Organizational Affiliation: 

Department of Pharmacology and Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.72 kDa 
• Atom Count: 2,480 
• Modelled Residue Count: 272 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	289	Homo sapiens	Mutation(s): 3  Gene Names: JAK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens) Explore O60674  Go to UniProtKB:  O60674
PHAROS:  O60674 GTEx:  ENSG00000096968

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IK1	B [auth A]	5-PHENYL-2-UREIDOTHIOPHENE-3-CARBOXAMIDE C12 H11 N3 O2 S PSVUSJKZJQMCSP-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.170 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.374	α = 90
b = 57.641	β = 109.94
c = 60.496	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Puleo, D.E., Schlessinger, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM007324
Gilead Sciences	United States	YG-003-13

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description