4QT1 | pdb_00004qt1

JAK3 kinase domain in complex with 1-[(3S)-1-isobutylsulfonyl-3-piperidyl]-3-(5H-pyrrolo[2,3-b]pyrazin-2-yl)urea

• PDB DOI: https://doi.org/10.2210/pdb4QT1/pdb

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


• Deposited: 2014-07-07 Released: 2015-05-27 
• Deposition Author(s): Kuglstatter, A., Shao, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Scaffold hopping towards potent and selective JAK3 inhibitors: discovery of novel C-5 substituted pyrrolopyrazines

De Vicente, J., Lemoine, R., Bartlett, M., Hermann, J.C., Hekmat-Nejad, M., Henningsen, R., Jin, S., Kuglstatter, A., Li, H., Lovey, A.J., Menke, J., Niu, L., Patel, V., Petersen, A., Setti, L., Shao, A., Tivitmahaisoon, P., Vu, M.D., Soth, M.

(2014) Bioorg Med Chem Lett 24: 4969-4975

• PubMed: 25262541 
• DOI: https://doi.org/10.1016/j.bmcl.2014.09.031
• Primary Citation Related Structures: 
  4QT1


• PubMed Abstract: 
  

  The discovery of a novel series of pyrrolopyrazines as JAK inhibitors with comparable enzyme and cellular activity to tofacitinib is described. The series was identified using a scaffold hopping approach aided by structure based drug design using principles of intramolecular hydrogen bonding for conformational restriction and targeting specific pockets for modulating kinase activity.

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Organizational Affiliation: 
• Small Molecule Research, Pharma Research & Early Development, pRED, Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, United States. Electronic address: [e-mail].
Roche Palo Alto, 3401 Hillview Ave, Palo Alto, CA 94304, United States.
Small Molecule Research, Pharma Research & Early Development, pRED, Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, United States.

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: 35.99 kDa 
• Atom Count: 2,329 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3C9	B [auth A]	1-{(3S)-1-[(2-methylpropyl)sulfonyl]piperidin-3-yl}-3-(5H-pyrrolo[2,3-b]pyrazin-2-yl)urea C16 H24 N6 O3 S UTTDMGAEOAWZGU-LBPRGKRZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3C9	BindingDB:  4QT1	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.921	α = 90
b = 75.703	β = 90
c = 89.729	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: 2015-05-27 
Deposition Author(s): Kuglstatter, A., Shao, A.

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description