Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.13 kDa 
• Atom Count: 4560 
• Modelled Residue Count: 530 
• Deposited Residue Count: 572 
• Unique protein chains: 1

2OIQ

Crystal Structure of chicken c-Src kinase domain in complex with the cancer drug imatinib.

• PDB DOI: 10.2210/pdb2OIQ/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-11 Released: 2007-03-20 
• Deposition Author(s): Seeliger, M.A., Nagar, B., Frank, F., Cao, X., Henderson, M.N., Kuriyan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.263 
• R-Value Work: 0.227 
• R-Value Observed: 0.232 

Literature

c-Src Binds to the Cancer Drug Imatinib with an Inactive Abl/c-Kit Conformation and a Distributed Thermodynamic Penalty.

Seeliger, M.A., Nagar, B., Frank, F., Cao, X., Henderson, M.N., Kuriyan, J.

(2007) Structure 15: 299-311

• PubMed: 17355866 
• DOI: 10.1016/j.str.2007.01.015
• Primary Citation of Related Structures:  
  2OIQ


• PubMed Abstract: 
  

The cancer drug imatinib inhibits the tyrosine kinases c-Abl, c-Kit, and the PDGF receptor. Imatinib is less effective against c-Src, which is difficult to understand because residues interacting with imatinib in crystal structures of Abl and c-Kit are conserved in c-Src. The crystal structure of the c-Src kinase domain in complex with imatinib closely resembles that of Abl*imatinib and c-Kit*imatinib, and differs significantly from the inactive "Src/CDK" conformation of the Src family kinases. Attempts to increase the affinity of c-Src for imatinib by swapping residues with the corresponding residues in Abl have not been successful, suggesting that the thermodynamic penalty for adoption of the imatinib-binding conformation by c-Src is distributed over a broad region of the structure. Two mutations that are expected to destabilize the inactive Src/CDK conformation increase drug sensitivity 15-fold, suggesting that the free-energy balance between different inactive states is a key to imatinib binding.

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Organizational Affiliation: 

Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 0  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STI	C [auth A]	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE C29 H31 N7 O KTUFNOKKBVMGRW-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STI	BindingDB:  2OIQ	Ki: min: 1.00e+4, max: 3.10e+4 (nM) from 2 assay(s)
		Kd: min: 1.00e+4, max: 3.98e+4 (nM) from 3 assay(s)
		IC50: min: 2784, max: 1.00e+5 (nM) from 3 assay(s)
	PDBBind:  2OIQ	Kd: 1.00e+4 (nM) from 1 assay(s)
	Binding MOAD:  2OIQ	Kd: 4.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.263 
• R-Value Work: 0.227 
• R-Value Observed: 0.232 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.078	α = 78.99
b = 63.373	β = 89.12
c = 74.474	γ = 90.1

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-11 
• Released Date: 2007-03-20 
Deposition Author(s): Seeliger, M.A., Nagar, B., Frank, F., Cao, X., Henderson, M.N., Kuriyan, J.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-04-15
  Changes: Data collection, Database references