4HVI

JAK3 kinase domain in complex with 2-Cyclopropyl-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((R)-1-methyl-2-oxo-2-piperidin-1-yl-ethyl)-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

3-Amido Pyrrolopyrazine JAK Kinase Inhibitors: Development of a JAK3 vs JAK1 Selective Inhibitor and Evaluation in Cellular and in Vivo Models.

Soth, M.Hermann, J.C.Yee, C.Alam, M.Barnett, J.W.Berry, P.Browner, M.F.Frank, K.Frauchiger, S.Harris, S.He, Y.Hekmat-Nejad, M.Hendricks, T.Henningsen, R.Hilgenkamp, R.Ho, H.Hoffman, A.Hsu, P.Y.Hu, D.Q.Itano, A.Jaime-Figueroa, S.Jahangir, A.Jin, S.Kuglstatter, A.Kutach, A.K.Liao, C.Lynch, S.Menke, J.Niu, L.Patel, V.Railkar, A.Roy, D.Shao, A.Shaw, D.Steiner, S.Sun, Y.Tan, S.L.Wang, S.Vu, M.D.

(2013) J Med Chem 56: 345-356

  • DOI: https://doi.org/10.1021/jm301646k
  • Primary Citation of Related Structures:  
    4HVD, 4HVG, 4HVH, 4HVI

  • PubMed Abstract: 

    The Janus kinases (JAKs) are involved in multiple signaling networks relevant to inflammatory diseases, and inhibition of one or more members of this class may modulate disease activity or progression. We optimized a new inhibitor scaffold, 3-amido-5-cyclopropylpyrrolopyrazines, to a potent example with reasonable kinome selectivity, including selectivity for JAK3 versus JAK1, and good biopharmaceutical properties. Evaluation of this analogue in cellular and in vivo models confirmed functional selectivity for modulation of a JAK3/JAK1-dependent IL-2 stimulated pathway over a JAK1/JAK2/Tyk2-dependent IL-6 stimulated pathway.


  • Organizational Affiliation

    Hoffmann-La Roche, 340 Kingsland Street, Nutley, New Jersey 07110, USA. michael.soth@roche.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
PHAROS:  P52333
GTEx:  ENSG00000105639 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52333
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
19S
Query on 19S

Download Ideal Coordinates CCD File 
B [auth A]2-cyclopropyl-N-[(2R)-1-oxo-1-(piperidin-1-yl)propan-2-yl]-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
C18 H23 N5 O2
STEKXUJMQOKLQV-LLVKDONJSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
19S PDBBind:  4HVI IC50: 68.9 (nM) from 1 assay(s)
BindingDB:  4HVI IC50: 69 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.094α = 90
b = 75.741β = 90
c = 89.915γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description