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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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: 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 selectivit ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE JAK3ABCD288Homo sapiensMutation(s): 2 
Gene Names: JAK3
EC: 2.7.10.2 (PDB Primary Data), 2.7.1.112 (PDB Primary Data)
Find proteins for P52333 (Homo sapiens)
Explore P52333 
Go to UniProtKB:  P52333
NIH Common Fund Data Resources
PHAROS  P52333
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 CCD File 
A, B, C, 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 CCD File 
C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A,B,C,DL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1NXIC50:  22   nM  Binding MOAD
1NXIC50:  22   nM  BindingDB
1NXIC50:  700   nM  BindingDB
1NXIC50 :  22   nM  PDBBind
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 

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