3ZEP

Crystal Structure of JAK3 Kinase Domain in Complex with a Pyrrolopyrazine-2-phenyl Ether Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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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

  • 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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE JAK3A, B, C, D288Homo sapiensMutation(s): 2 
Gene Names: JAK3
EC: 2.7.10.2 (PDB Primary Data), 2.7.1.112 (PDB Primary Data)
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
1NX
Query on 1NX
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
I [auth D]		2-[[(3R)-3-acetamido-2,3-dihydro-1H-inden-5-yl]oxy]-N-[(1S)-1-cyclopropylethyl]-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
C23 H25 N5 O3
ZLMYXZMBDPHCEG-HXPMCKFVSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A, B, C, D L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
1NX BindingDB:  3ZEP IC50: min: 22, max: 700 (nM) from 2 assay(s)
Binding MOAD:  3ZEP IC50: 22 (nM) from 1 assay(s)
PDBBind:  3ZEP IC50: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.554α = 90
b = 114.076β = 96.82
c = 104.196γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references