1T46

STRUCTURAL BASIS FOR THE AUTOINHIBITION AND STI-571 INHIBITION OF C-KIT TYROSINE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.213 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase.

Mol, C.D.Dougan, D.R.Schneider, T.R.Skene, R.J.Kraus, M.L.Scheibe, D.N.Snell, G.P.Zou, H.Sang, B.C.Wilson, K.P.

(2004) J Biol Chem 279: 31655-31663

  • DOI: https://doi.org/10.1074/jbc.M403319200
  • Primary Citation of Related Structures:  
    1T45, 1T46

  • PubMed Abstract: 

    The activity of the c-Kit receptor protein-tyrosine kinase is tightly regulated in normal cells, whereas deregulated c-Kit kinase activity is implicated in the pathogenesis of human cancers. The c-Kit juxtamembrane region is known to have an autoinhibitory function; however the precise mechanism by which c-Kit is maintained in an autoinhibited state is not known. We report the 1.9-A resolution crystal structure of native c-Kit kinase in an autoinhibited conformation and compare it with active c-Kit kinase. Autoinhibited c-Kit is stabilized by the juxtamembrane domain, which inserts into the kinase-active site and disrupts formation of the activated structure. A 1.6-A crystal structure of c-Kit in complex with STI-571 (Imatinib or Gleevec) demonstrates that inhibitor binding disrupts this natural mechanism for maintaining c-Kit in an autoinhibited state. Together, these results provide a structural basis for understanding c-Kit kinase autoinhibition and will facilitate the structure-guided design of specific inhibitors that target the activated and autoinhibited conformations of c-Kit kinase.


  • Organizational Affiliation

    Syrrx, Inc., San Diego, California, 92121, USA. clifford.mol@syrrx.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homo sapiens v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog313Homo sapiensMutation(s): 0 
Gene Names: kit
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
PHAROS:  P10721
GTEx:  ENSG00000157404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10721
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
STI BindingDB:  1T46 Ki: min: 14, max: 7.10e+4 (nM) from 5 assay(s)
Kd: min: 3, max: 3000 (nM) from 14 assay(s)
IC50: min: 16, max: 1.00e+4 (nM) from 23 assay(s)
EC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.213 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.089α = 90
b = 70.089β = 90
c = 127.88γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted STIClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-15
    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: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Structure summary