1Y57

Structure of unphosphorylated c-Src in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of a c-Src Complex in an Active Conformation Suggests Possible Steps in c-Src Activation

Cowan-Jacob, S.W.Fendrich, G.Manley, P.W.Jahnke, W.Fabbro, D.Liebetanz, J.Meyer, T.

(2005) Structure 13: 861-871

  • DOI: 10.1016/j.str.2005.03.012

  • PubMed Abstract: 
  • The regulation of the activity of Abl and Src family tyrosine kinases is mediated by intramolecular interactions between the SH3, SH2, and kinase (SH1) domains. We have determined the crystal structure of an unphosphorylated form of c-Src in which th ...

    The regulation of the activity of Abl and Src family tyrosine kinases is mediated by intramolecular interactions between the SH3, SH2, and kinase (SH1) domains. We have determined the crystal structure of an unphosphorylated form of c-Src in which the SH2 domain is not bound to the C-terminal tail. This results in an open structure where the kinase domain adopts an active conformation and the C terminus binds within a hydrophobic pocket in the C-terminal lobe. NMR binding studies support the hypothesis that an N-terminal myristate could bind in this pocket, as observed for Abl, suggesting that c-Src may also be regulated by myristate binding. In addition, the structure contains a des-methyl analog of the antileukemia drug imatinib (STI571; Gleevec). This structure reveals why the drug shows a low affinity for active kinase conformations, contributing to its excellent kinase selectivity profile.


    Organizational Affiliation

    Discovery Technologies, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland. sandra.jacob@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A
452Homo sapiensGene Names: SRC (SRC1)
EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens)
Go to Gene View: SRC
Go to UniProtKB:  P12931
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MPZ
Query on MPZ

Download SDF File 
Download CCD File 
A
4-[(4-METHYLPIPERAZIN-1-YL)METHYL]-N-{3-[(4-PYRIDIN-3-YLPYRIMIDIN-2-YL)AMINO]PHENYL}BENZAMIDE
4-[(4-METHYL-1-PIPERAZINYL)METHYL]-N-[3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]AMINO]PHENYL]-BENZAMIDE
C28 H29 N7 O
JHMBUEWQJDGKGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MPZIC50: 7800 nM (100) BINDINGDB
MPZIC50: 1633 nM BINDINGMOAD
MPZIC50: 1633 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.212α = 90.00
b = 106.212β = 90.00
c = 123.731γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2015-04-15
    Type: Database references