6WIW

c-Src Bound to ATP-Competitive Inhibitor I14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture.

Fang, L.Vilas-Boas, J.Chakraborty, S.Potter, Z.E.Register, A.C.Seeliger, M.A.Maly, D.J.

(2020) ACS Chem Biol 15: 2005-2016

  • DOI: 10.1021/acschembio.0c00429
  • Primary Citation of Related Structures:  
    6WIW

  • PubMed Abstract: 
  • Small molecule kinase inhibitors that stabilize distinct ATP-binding site conformations can differentially modulate the global conformation of Src-family kinases (SFKs). However, it is unclear which specific ATP-binding site contacts are responsible ...

    Small molecule kinase inhibitors that stabilize distinct ATP-binding site conformations can differentially modulate the global conformation of Src-family kinases (SFKs). However, it is unclear which specific ATP-binding site contacts are responsible for modulating the global conformation of Src-family kinases (SFKs) and whether these inhibitor-mediated allosteric effects are general to other tyrosine kinases. Here, we describe the development of chemical probes that allow us to deconvolute which features in the ATP-binding site are responsible for the allosteric modulation of the global conformation of Src. We find that the ability of an inhibitor to modulate the global conformation of Src's regulatory domain-catalytic domain module relies mainly on the influence it has on the conformation of a structural element called helix C. Furthermore, by developing a set of orthogonal probes that target a drug-sensitized Src variant, we show that stabilizing Src's helix C in an active conformation is sufficient to promote a Src-mediated, phosphotransferase-independent alteration in cell morphology. Finally, we report that ATP-competitive, conformation-selective inhibitors can influence the global conformation of tyrosine kinases beyond the SFKs, suggesting that the allosteric networks we observe in Src are conserved in kinases that have a similar regulatory architecture. Taken together, our study highlights that an ATP-competitive inhibitor's interactions with helix C can have a major influence on the global conformation of some tyrosine kinases in vitro and in cells.


    Organizational Affiliation

    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase SrcAB286Gallus gallusMutation(s): 0 
Gene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I14
Query on I14

Download CCD File 
A, B
N-(3-{[4-amino-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]ethynyl}-4-methylphenyl)acetamide
C20 H21 N5 O2
JQKPZHMYPLLZEN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.151α = 78.24
b = 63.872β = 89.668
c = 74.875γ = 90.208
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119437
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103962

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references