Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 37.02 kDa 
• Atom Count: 2,575 
• Modelled Residue Count: 284 
• Deposited Residue Count: 311 
• Unique protein chains: 1

 3JY9

Janus Kinase 2 Inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb3JY9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2009-09-21 Released: 2009-12-01 
• Deposition Author(s): Zuccola, H.J., Ledeboer, M.W., Pierce, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.271 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 

Literature

Janus kinase 2 inhibitors. Synthesis and characterization of a novel polycyclic azaindole.

Wang, T., Duffy, J.P., Wang, J., Halas, S., Salituro, F.G., Pierce, A.C., Zuccola, H.J., Black, J.R., Hogan, J.K., Jepson, S., Shlyakter, D., Mahajan, S., Gu, Y., Hoock, T., Wood, M., Furey, B.F., Frantz, J.D., Dauffenbach, L.M., Germann, U.A., Fan, B., Namchuk, M., Bennani, Y.L., Ledeboer, M.W.

(2009) J Med Chem 52: 7938-7941

• PubMed: 20014869 
• DOI: https://doi.org/10.1021/jm901383u
• Primary Citation of Related Structures:  
  3JY9


• PubMed Abstract: 
  

The synthesis and characterization of a novel polycyclic azaindole based derivative is disclosed, and its binding to JAK2 is described. The compound is further evaluated for its ability to block the EPO/JAK2 signaling cascade in vitro and in vivo.

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Organizational Affiliation: 

Vertex Pharmaceuticals Inc., Cambridge, Massachusetts 02139-4242, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	311	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JZH	B [auth A]	(3S)-3-(4-hydroxyphenyl)-1,5-dihydro-1,5,12-triazabenzo[4,5]cycloocta[1,2,3-cd]inden-4(3H)-one C21 H15 N3 O2 LGIBDQRYOFBMTC-SFHVURJKSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
JZH	Binding MOAD:  3JY9	Ki: 1 (nM) from 1 assay(s)
	PDBBind:  3JY9	Ki: 1 (nM) from 1 assay(s)
	BindingDB:  3JY9	Ki: 1 (nM) from 1 assay(s)
		IC50: 270 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.271 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.103	α = 90
b = 101.257	β = 90
c = 68.488	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
d*TREK	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Zuccola, H.J., Ledeboer, M.W., Pierce, A.C.

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-04-03
  Changes: Experimental preparation