3DQW

c-Src kinase domain Thr338Ile mutant in complex with ATPgS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Activation of tyrosine kinases by mutation of the gatekeeper threonine.

Azam, M.Seeliger, M.A.Gray, N.S.Kuriyan, J.Daley, G.Q.

(2008) Nat Struct Mol Biol 15: 1109-1118

  • DOI: 10.1038/nsmb.1486
  • Primary Citation of Related Structures:  
    3DQX, 3DQW

  • PubMed Abstract: 
  • Protein kinases targeted by small-molecule inhibitors develop resistance through mutation of the 'gatekeeper' threonine residue of the active site. Here we show that the gatekeeper mutation in the cellular forms of c-ABL, c-SRC, platelet-derived growth factor receptor-alpha and -beta, and epidermal growth factor receptor activates the kinase and promotes malignant transformation of BaF3 cells ...

    Protein kinases targeted by small-molecule inhibitors develop resistance through mutation of the 'gatekeeper' threonine residue of the active site. Here we show that the gatekeeper mutation in the cellular forms of c-ABL, c-SRC, platelet-derived growth factor receptor-alpha and -beta, and epidermal growth factor receptor activates the kinase and promotes malignant transformation of BaF3 cells. Structural analysis reveals that a network of hydrophobic interactions-the hydrophobic spine-characteristic of the active kinase conformation is stabilized by the gatekeeper substitution. Substitution of glycine for the residues constituting the spine disrupts the hydrophobic connectivity and inactivates the kinase. Furthermore, a small-molecule inhibitor that maximizes complementarity with the dismantled spine (compound 14) inhibits the gatekeeper mutation of BCR-ABL-T315I. These results demonstrate that mutation of the gatekeeper threonine is a common mechanism of activation for tyrosine kinases and provide structural insights to guide the development of next-generation inhibitors.


    Organizational Affiliation

    Karp research building, 7th floor, Division of Pediatric Hematology/Oncology, Children's Hospital of Boston, Massachusetts 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src ABCD286Gallus gallusMutation(s): 1 
Gene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A,B,C,DL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PTR-TΔS:  18.100000381469727   kJ/mol  BindingDB
PTRΔG:  21.399999618530273   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.42α = 90
b = 103.65β = 103.94
c = 83.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-15
    Changes: Non-polymer description