5UT6

JAK2 JH2 in complex with a diaminopyrimidine

• PDB DOI: https://doi.org/10.2210/pdb5UT6/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: 1.65 Å
• R-Value Free: 0.206 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Literature

JAK2 JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules.

Newton, A.S., Deiana, L., Puleo, D.E., Cisneros, J.A., Cutrona, K.J., Schlessinger, J., Jorgensen, W.L.

(2017) ACS Med Chem Lett 8: 614-617

• PubMed: 28626520 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00154
• Primary Citation of Related Structures:  
  5UT4, 5UT5, 5UT6


• PubMed Abstract: 
  

  A competitive fluorescence polarization (FP) assay is reported for determining binding affinities of probe molecules with the pseudokinase JAK2 JH2 allosteric site. The syntheses of the fluorescent 5 and 6 used in the assay are reported as well as K _d results for 10 compounds, including JNJ7706621, NVP-BSK805, and filgotinib (GLPG0634). X-ray crystal structures of JAK2 JH2 in complex with NVP-BSK805, filgotinib, and diaminopyrimidine 8 elucidate the binding poses.

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Organizational Affiliation: 

Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.03 kDa 
• Atom Count: 2,466 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8MY	B [auth A]	4-({4-amino-6-[3-(hydroxymethyl)-1H-pyrazol-1-yl]pyrimidin-2-yl}amino)benzonitrile C15 H13 N7 O NMBKNACBCUDEER-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
8MY	BindingDB:  5UT6	Kd: 5.73e+4 (nM) from 1 assay(s)
	Binding MOAD:  5UT6	Kd: 5.73e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.206 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.371	α = 90
b = 57.642	β = 110.24
c = 60.682	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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