4I6Q | pdb_00004i6q

JAK3 kinase domain in complex with 2-Phenoxy-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((S)-1-cyclopropyl-ethyl)-amide

• PDB DOI: https://doi.org/10.2210/pdb4I6Q/pdb

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


• Deposited: 2012-11-30 Released: 2013-10-16 
• Deposition Author(s): Kuglstatter, A., Shao, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Discovery of a series of novel 5H-pyrrolo[2,3-b]pyrazine-2-phenyl ethers, as potent JAK3 kinase inhibitors.

Jaime-Figueroa, S., De Vicente, J., Hermann, J., Jahangir, A., Jin, S., Kuglstatter, A., Lynch, S.M., Menke, J., Niu, L., Patel, V., Shao, A., Soth, M., Vu, M.D., Yee, C.

(2013) Bioorg Med Chem Lett 23: 2522-2526

• PubMed: 23541670 
• DOI: https://doi.org/10.1016/j.bmcl.2013.03.015
• Primary Citation Related Structures: 
  3ZEP, 4I6Q


• PubMed Abstract: 
  

  We report the discovery of a novel series of ATP-competitive Janus kinase 3 (JAK3) inhibitors based on the 5H-pyrrolo[2,3-b]pyrazine scaffold. The initial leads in this series, compounds 1a and 1h, showed promising potencies, but a lack of selectivity against other isoforms in the JAK family. Computational and crystallographic analysis suggested that the phenyl ether moiety possessed a favorable vector to achieve selectivity. Exploration of this vector resulted in the identification of 12b and 12d, as potent JAK3 inhibitors, demonstrating improved JAK family and kinase selectivity.

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Organizational Affiliation: 
• Hoffmann-La Roche Inc., pRED, Pharma Research & Early Development, Small Molecule Research, Discovery Chemistry, 340 Kingsland Street, Nutley, NJ 07110-1199, USA. [e-mail]

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: 36.07 kDa 
• Atom Count: 2,347 
• Modeled Residue Count: 277 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK3	A	314	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1DT	C [auth A]	N-[(1S)-1-cyclopropylethyl]-2-phenoxy-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide C18 H18 N4 O2 TUNBOTWJAARGCJ-NSHDSACASA-N
PHU	B [auth A]	1-phenylurea C7 H8 N2 O LUBJCRLGQSPQNN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.874	α = 90
b = 75.646	β = 90
c = 89.27	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Kuglstatter, A., Shao, A.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description