3LXN

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: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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
  • Primary Citation of Related Structures:  
    3LXP, 3LXK, 3LXL, 3LXN

  • 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 reported recently with the clinical compound CP-690550, the structures of both TYK2 and JAK3 with CP-690550 have remained outstanding ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-receptor tyrosine-protein kinase TYK2A318Homo sapiensMutation(s): 5 
Gene Names: TYK2
EC: 2.7.10.2
Find proteins for P29597 (Homo sapiens)
Explore P29597 
Go to UniProtKB:  P29597
NIH Common Fund Data Resources
PHAROS:  P29597
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MI1
Query on MI1

Download Ideal Coordinates CCD File 
B [auth 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MI1IC50:  75   nM  BindingDB
MI1IC50:  1200   nM  BindingDB
MI1Ki:  4.400000095367432   nM  Binding MOAD
MI1IC50:  8.899999618530273   nM  BindingDB
MI1Kd:  4.800000190734863   nM  BindingDB
MI1IC50:  10.399999618530273   nM  BindingDB
MI1IC50:  36   nM  BindingDB
MI1IC50:  41   nM  BindingDB
MI1Ki:  7.800000190734863   nM  BindingDB
MI1IC50:  489   nM  BindingDB
MI1IC50:  34   nM  BindingDB
MI1IC50:  35   nM  BindingDB
MI1IC50:  52   nM  BindingDB
MI1IC50:  230   nM  BindingDB
MI1Kd:  10000   nM  BindingDB
MI1Kd:  620   nM  BindingDB
MI1IC50:  472   nM  BindingDB
MI1IC50:  409   nM  BindingDB
MI1IC50:  9   nM  BindingDB
MI1IC50:  10   nM  BindingDB
MI1Kd:  250   nM  BindingDB
MI1IC50:  13   nM  BindingDB
MI1IC50:  229   nM  BindingDB
MI1Ki:  4.389999866485596   nM  BindingDB
MI1IC50:  176   nM  BindingDB
MI1IC50:  12   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.306α = 90
b = 74.262β = 90
c = 106.46γ = 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  (Full details and data files)

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