3JY9 | pdb_00003jy9

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 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

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 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.

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 
• Modeled Residue Count: 284 
• Deposited Residue Count: 311 
• Unique protein chains: 1

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 GTEx:  ENSG00000096968

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.271 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

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
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.4: 2024-04-03
  Changes: Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary