4QT1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmcl.2014.09.031
  • Primary Citation of 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.


  • Organizational Affiliation

    Small Molecule Research, Pharma Research & Early Development, pRED, Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, United States. Electronic address: javier.devicente@novartis.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK3314Homo sapiensMutation(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
GTEx:  ENSG00000105639 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52333
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3C9
Query on 3C9

Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.921α = 90
b = 75.703β = 90
c = 89.729γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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