Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.59 kDa 
• Atom Count: 3976 
• Residue Count: 452 
• Unique protein chains: 1

1Y57

Structure of unphosphorylated c-Src in complex with an inhibitor

• DOI: 10.2210/pdb1Y57/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2004-12-02 Released: 2005-06-21 
• Deposition Author(s): Cowan-Jacob, S.W., Fendrich, G., Manley, P.W., Jahnke, W., Fabbro, D., Liebetanz, J., Meyer, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.213 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

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

• PubMed: 15939018 
• DOI: 10.1016/j.str.2005.03.012
• Primary Citation of Related Structures:  
  1Y57


• 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 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.

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Organizational Affiliation: 

Discovery Technologies, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	452	Homo sapiens	Mutation(s): 0  Gene Names: SRC, SRC1 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P12931 (Homo sapiens) Explore P12931  Go to UniProtKB:  P12931
NIH Common Fund Data Resources
PHAROS  P12931 GTEx  ENSG00000197122

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPZ	A	4-[(4-METHYLPIPERAZIN-1-YL)METHYL]-N-{3-[(4-PYRIDIN-3-YLPYRIMIDIN-2-YL)AMINO]PHENYL}BENZAMIDE C28 H29 N7 O JHMBUEWQJDGKGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MPZ	IC50:  1633   nM  Binding MOAD
MPZ	IC50 :  1633   nM  PDBBind
MPZ	IC50:  7800   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.213 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.212	α = 90
b = 106.212	β = 90
c = 123.731	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-02 
• Released Date: 2005-06-21 
Deposition Author(s): Cowan-Jacob, S.W., Fendrich, G., Manley, P.W., Jahnke, W., Fabbro, D., Liebetanz, J., Meyer, T.

Revision History 

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