5WFJ | pdb_00005wfj

THE JAK3 KINASE DOMAIN IN COMPLEX WITH A COVALENT INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb5WFJ/pdb

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


• Deposited: 2017-07-12 Released: 2017-10-04 
• Deposition Author(s): Sack, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Discovery of highly potent, selective, covalent inhibitors of JAK3.

Kempson, J., Ovalle, D., Guo, J., Wrobleski, S.T., Lin, S., Spergel, S.H., Duan, J.J., Jiang, B., Lu, Z., Das, J., Yang, B.V., Hynes, J., Wu, H., Tokarski, J., Sack, J.S., Khan, J., Schieven, G., Blatt, Y., Chaudhry, C., Salter-Cid, L.M., Fura, A., Barrish, J.C., Carter, P.H., Pitts, W.J.

(2017) Bioorg Med Chem Lett 27: 4622-4625

• PubMed: 28927786 
• DOI: https://doi.org/10.1016/j.bmcl.2017.09.023
• Primary Citation Related Structures: 
  5WFJ


• PubMed Abstract: 
  

  A useful and novel set of tool molecules have been identified which bind irreversibly to the JAK3 active site cysteine residue. The design was based on crystal structure information and a comparative study of several electrophilic warheads.

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Organizational Affiliation: 
• Bristol-Myers Squibb Research and Development, Princeton, NJ 08543-4000, USA. Electronic address: [e-mail].
Bristol-Myers Squibb Research and Development, Princeton, NJ 08543-4000, 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: 33.59 kDa 
• Atom Count: 2,139 
• Modeled Residue Count: 265 
• 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): 3  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
9Z4	B [auth A]	4-({[3-(propanoylamino)phenyl]methyl}amino)pyrrolo[1,2-b]pyridazine-3-carboxamide C18 H19 N5 O2 NLMYDZAEGAXRHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.34	α = 90
b = 75.69	β = 90
c = 88.95	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Sack, J.

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary