4I6Q

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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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

  • DOI: https://doi.org/10.1016/j.bmcl.2013.03.015
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Hoffmann-La Roche Inc., pRED, Pharma Research & Early Development, Small Molecule Research, Discovery Chemistry, 340 Kingsland Street, Nutley, NJ 07110-1199, USA. saul.jaime@roche.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK3A314Homo 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
PHAROS:  P52333
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52333
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1DT
Query on 1DT
Download Ideal Coordinates CCD File 
C [auth A]N-[(1S)-1-cyclopropylethyl]-2-phenoxy-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
C18 H18 N4 O2
TUNBOTWJAARGCJ-NSHDSACASA-N		 Ligand Interaction
PHU
Query on PHU
Download Ideal Coordinates CCD File 
B [auth A]1-phenylurea
C7 H8 N2 O
LUBJCRLGQSPQNN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1DT PDBBind:  4I6Q IC50: 30 (nM) from 1 assay(s)
Binding MOAD:  4I6Q IC50: 30 (nM) from 1 assay(s)
BindingDB:  4I6Q IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.874α = 90
b = 75.646β = 90
c = 89.27γ = 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 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release