Crystal Structure of the ZAP-70 Kinase Domain in Complex with Staurosporine

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 

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The Three-dimensional Structure of the ZAP-70 Kinase Domain in Complex with Staurosporine: IMPLICATIONS FOR THE DESIGN OF SELECTIVE INHIBITORS

Jin, L.Pluskey, S.Petrella, E.C.Cantin, S.M.Gorga, J.C.Rynkiewicz, M.J.Pandey, P.Strickler, J.E.Babine, R.E.Weaver, D.T.Seidl, K.J.

(2004) J Biol Chem 279: 42818-42825

  • DOI: https://doi.org/10.1074/jbc.M407096200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The ZAP-70 tyrosine kinase plays a critical role in T cell activation and the immune response and therefore is a logical target for immunomodulatory therapies. Although the crystal structure of the tandem Src homology-2 domains of human ZAP-70 in complex with a peptide derived from the zeta subunit of the T cell receptor has been reported (Hatada, M. H., Lu, X., Laird, E. R., Green, J., Morgenstern, J. P., Lou, M., Marr, C. S., Phillips, T. B., Ram, M. K., Theriault, K., Zoller, M. J., and Karas, J. L. (1995) Nature 377, 32-38), the structure of the kinase domain has been elusive to date. We crystallized and determined the three-dimensional structure of the catalytic subunit of ZAP-70 as a complex with staurosporine to 2.3 A resolution, utilizing an active kinase domain containing residues 327-606 identified by systematic N- and C-terminal truncations. The crystal structure shows that this ZAP-70 kinase domain is in an active-like conformation despite the lack of tyrosine phosphorylation in the activation loop. The unique features of the ATP-binding site, identified by structural and sequence comparison with other kinases, will be useful in the design of ZAP-70-selective inhibitors.

  • Organizational Affiliation

    Daiichi Asubio Medical Research Laboratories LLC, Cambridge, MA 02139, USA. lei.jin@daiamed.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ZAP-70287Homo sapiensMutation(s): 0 
Gene Names: ZAP70SRK
UniProt & NIH Common Fund Data Resources
Find proteins for P43403 (Homo sapiens)
Explore P43403 
Go to UniProtKB:  P43403
PHAROS:  P43403
GTEx:  ENSG00000115085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43403
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on STU

Download Ideal Coordinates CCD File 
C28 H26 N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
STU Binding MOAD:  1U59 IC50: 55.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.056α = 90
b = 57.064β = 90
c = 125.133γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description