3LXK

Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and thermodynamic characterization of the TYK2 and JAK3 kinase domains in complex with CP-690550 and CMP-6.

Chrencik, J.E.Patny, A.Leung, I.K.Korniski, B.Emmons, T.L.Hall, T.Weinberg, R.A.Gormley, J.A.Williams, J.M.Day, J.E.Hirsch, J.L.Kiefer, J.R.Leone, J.W.Fischer, H.D.Sommers, C.D.Huang, H.C.Jacobsen, E.J.Tenbrink, R.E.Tomasselli, A.G.Benson, T.E.

(2010) J Mol Biol 400: 413-433

  • DOI: 10.1016/j.jmb.2010.05.020
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Janus kinases (JAKs) are critical regulators of cytokine pathways and attractive targets of therapeutic value in both inflammatory and myeloproliferative diseases. Although the crystal structures of active JAK1 and JAK2 kinase domains have been repor ...

    Janus kinases (JAKs) are critical regulators of cytokine pathways and attractive targets of therapeutic value in both inflammatory and myeloproliferative diseases. Although the crystal structures of active JAK1 and JAK2 kinase domains have been reported recently with the clinical compound CP-690550, the structures of both TYK2 and JAK3 with CP-690550 have remained outstanding. Here, we report the crystal structures of TYK2, a first in class structure, and JAK3 in complex with PAN-JAK inhibitors CP-690550 ((3R,4R)-3-[4-methyl-3-[N-methyl-N-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl]-3-oxopropionitrile) and CMP-6 (tetracyclic pyridone 2-t-butyl-9-fluoro-3,6-dihydro-7H-benz[h]-imidaz[4,5-f]isoquinoline-7-one), both of which bind in the ATP-binding cavities of both JAK isozymes in orientations similar to that observed in crystal structures of JAK1 and JAK2. Additionally, a complete thermodynamic characterization of JAK/CP-690550 complex formation was completed by isothermal titration calorimetry, indicating the critical role of the nitrile group from the CP-690550 compound. Finally, computational analysis using WaterMap further highlights the critical positioning of the CP-690550 nitrile group in the displacement of an unfavorable water molecule beneath the glycine-rich loop. Taken together, the data emphasize the outstanding properties of the kinome-selective JAK inhibitor CP-690550, as well as the challenges in obtaining JAK isozyme-selective inhibitors due to the overall structural and sequence similarities between the TYK2, JAK1, JAK2 and JAK3 isozymes. Nevertheless, subtle amino acid variations of residues lining the ligand-binding cavity of the JAK enzymes, as well as the global positioning of the glycine-rich loop, might provide the initial clues to obtaining JAK-isozyme selective inhibitors.


    Organizational Affiliation

    Pfizer Inc. 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA. jill.chrencik@pfizer.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK3A327Homo sapiensMutation(s): 1 
Gene Names: JAK3
EC: 2.7.10.2
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MI1
Query on MI1

Download CCD File 
A
3-{(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}-3-oxopropanenitrile
C16 H20 N6 O
UJLAWZDWDVHWOW-YPMHNXCESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MI1IC50:  28   nM  BindingDB
MI1IC50:  1.2000000476837158   nM  BindingDB
MI1IC50:  24   nM  BindingDB
MI1IC50:  48   nM  BindingDB
MI1Ki:  0.23999999463558197   nM  BindingDB
MI1Ki:  0.20000000298023224   nM  Binding MOAD
MI1IC50:  3.200000047683716   nM  BindingDB
MI1IC50:  2   nM  BindingDB
MI1IC50:  0.3499999940395355   nM  BindingDB
MI1IC50:  30   nM  BindingDB
MI1IC50:  3.5   nM  BindingDB
MI1IC50:  55   nM  BindingDB
MI1IC50:  56   nM  BindingDB
MI1IC50:  2.200000047683716   nM  BindingDB
MI1IC50:  54   nM  BindingDB
MI1IC50:  0.6000000238418579   nM  BindingDB
MI1IC50:  45   nM  BindingDB
MI1Kd :  0.1599999964237213   nM  PDBBind
MI1IC50:  5   nM  BindingDB
MI1Kd:  0.699999988079071   nM  BindingDB
MI1IC50:  1.600000023841858   nM  BindingDB
MI1IC50:  4   nM  BindingDB
MI1Ki:  2200   nM  BindingDB
MI1Kd:  0.1599999964237213   nM  BindingDB
MI1Kd:  2.200000047683716   nM  BindingDB
MI1IC50:  0.800000011920929   nM  BindingDB
MI1IC50:  8   nM  BindingDB
MI1IC50:  1.399999976158142   nM  BindingDB
MI1IC50:  156   nM  BindingDB
MI1IC50:  0.9599999785423279   nM  BindingDB
MI1IC50:  13   nM  BindingDB
MI1Ki:  1   nM  BindingDB
MI1IC50:  0.3400000035762787   nM  BindingDB
MI1IC50:  11   nM  BindingDB
MI1IC50:  20   nM  BindingDB
MI1IC50:  3.299999952316284   nM  BindingDB
MI1IC50:  1   nM  BindingDB
MI1Ki:  0.4000000059604645   nM  BindingDB
MI1IC50:  0.28999999165534973   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.77α = 90
b = 75.339β = 90
c = 88.392γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance