5VO6 | pdb_00005vo6

CRYSTAL STRUCTURE OF JAK3 KINASE DOMAIN IN COMPLEX WITH A PYRROLOPYRIDAZINE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb5VO6/pdb

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


• Deposited: 2017-05-02 Released: 2017-05-31 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.284 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Discovery of potent and efficacious pyrrolopyridazines as dual JAK1/3 inhibitors.

Hynes, J., Wu, H., Kempson, J., Duan, J.J., Lu, Z., Jiang, B., Stachura, S., Tokarski, J.S., Sack, J.S., Khan, J.A., Lippy, J.S., Zhang, R.F., Pitt, S., Shen, G., Gillooly, K., McIntyre, K., Carter, P.H., Barrish, J.C., Nadler, S.G., Salter-Cid, L.M., Fura, A., Schieven, G.L., Pitts, W.J., Wrobleski, S.T.

(2017) Bioorg Med Chem Lett 27: 3101-3106

• PubMed: 28539220 
• DOI: https://doi.org/10.1016/j.bmcl.2017.05.043
• Primary Citation Related Structures: 
  5VO6


• PubMed Abstract: 
  

  A series of potent dual JAK1/3 inhibitors have been developed from a moderately selective JAK3 inhibitor. Substitution at the C6 position of the pyrrolopyridazine core with aryl groups provided exceptional biochemical potency against JAK1 and JAK3 while maintaining good selectivity against JAK2 and Tyk2. Translation to in vivo efficacy was observed in a murine model of chronic inflammation. X-ray co-crystal structure determination confirmed the presumed inhibitor binding orientation in JAK3. Efforts to reduce hERG channel inhibition will be described.

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Organizational Affiliation: 
• Research and Development, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, NJ 08543, USA. Electronic address: [e-mail].
Research and Development, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, NJ 08543, 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: 33.63 kDa 
• Atom Count: 2,166 
• Modeled Residue Count: 271 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK3	A	293	Homo sapiens	Mutation(s): 2  Gene Names: JAK3 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P52333 (Homo sapiens) Explore P52333  Go to UniProtKB:  P52333
PHAROS:  P52333 GTEx:  ENSG00000105639

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9J4	B [auth A]	4-{[(1R,3S)-3-amino-2,2,3-trimethylcyclopentyl]amino}-6-phenylpyrrolo[1,2-b]pyridazine-3-carboxamide C22 H27 N5 O DIFGSGNUHRNWPK-GCJKJVERSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9J4	BindingDB:  5VO6	IC50: min: 0.9, max: 200 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.284 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.35	α = 90
b = 75.04	β = 90
c = 86.96	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Sack, J.S.

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2017-06-21
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references