6M9H | pdb_00006m9h

JAK2 JH2 in complex with diaminopyrimidine JAK040

• PDB DOI: https://doi.org/10.2210/pdb6M9H/pdb

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


• Deposited: 2018-08-23 Released: 2018-09-05 
• Deposition Author(s): Puleo, D.E., Schlessinger, J., Jorgensen, W.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

JAK2 JH2 Binders

Puleo, D.E., Schlessinger, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.61 kDa 
• Atom Count: 2,438 
• Modeled Residue Count: 273 
• 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
J9D (Subject of Investigation/LOI)	B [auth A]	4-({4-amino-6-[4-(2-hydroxyethyl)-1H-imidazol-1-yl]pyrimidin-2-yl}amino)benzonitrile C16 H15 N7 O OVFXXQZOTWTSJA-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.298	α = 90
b = 57.6	β = 110.17
c = 60.691	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: 2018-09-05 
Deposition Author(s): Puleo, D.E., Schlessinger, J., Jorgensen, W.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM007324
Other private	United States	YG-003-13
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM32136

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2018-11-21
  Changes: Author supporting evidence, Data collection, Structure summary
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references