Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33222.14 
• Atom Count: 2071 
• Residue Count: 286 
• Unique protein chains: 1

3EL7

Crystal structure of c-Src in complex with pyrazolopyrimidine 3

• DOI: 10.2210/pdb3EL7/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli


• Deposited: 2008-09-20 Released: 2008-10-28 
• Deposition Author(s): Dar, A.C., Lopez, M.S., Shokat, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.288 
• R-Value Work: 0.220 

Literature

Small molecule recognition of c-Src via the Imatinib-binding conformation.

Dar, A.C., Lopez, M.S., Shokat, K.M.

(2008) Chem.Biol. 15: 1015-1022

• PubMed: 18940662 
• DOI: 10.1016/j.chembiol.2008.09.007
• Primary Citation of Related Structures:  
  3EL8
• Also Cited By: 3QLG, 3QLF


• PubMed Abstract: 
  

The cancer drug, Imatinib, is a selective Abl kinase inhibitor that does not inhibit the closely related kinase c-Src. This one drug and its ability to selectively inhibit Abl over c-Src has been a guiding principle in virtually all kinase drug discovery efforts in the last 15 years. A prominent hypothesis explaining the selectivity of Imatinib is that Abl has an intrinsic ability to adopt an inactive conformation (termed DFG-out), whereas c-Src appears to pay a high intrinsic energetic penalty for adopting this conformation, effectively excluding Imatinib from its ATP pocket. This explanation of the difference in binding affinity of Imatinib for Abl versus c-Src makes the striking prediction that it would not be possible to design an inhibitor that binds to the DFG-out conformation of c-Src with high affinity. We report the discovery of a series of such inhibitors. We use structure-activity relationships and X-ray crystallography to confirm our findings. These studies suggest that small molecules are capable of inducing the generally unfavorable DFG-out conformation in c-Src. Structural comparison between c-Src in complex with these inhibitors allows us to speculate on the differential selectivity of Imatinib for c-Src and Abl.

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Organizational Affiliation: 

Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, Genentech Hall, 600 16(th) Street, University of California, San Francisco, San Francisco, CA 94158, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PD3	A	1-{3-[(4-amino-1-cyclopentyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)methyl]phenyl}-3-[3-(trifluoromethyl)phenyl]urea C25 H24 F3 N7 O RKZUINFXRREENO-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PD3	IC50: 480 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.288 
• R-Value Work: 0.220 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.360	α = 90.00
b = 63.130	β = 91.90
c = 56.050	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data scaling
CNS	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-20 
• Released Date: 2008-10-28 
• Deposition Author(s): Dar, A.C., Lopez, M.S., Shokat, K.M.

Revision History 

• Version 1.0: 2008-10-28
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2011-12-07
  Type: Database references