Src kinase in complex with inhibitor AP23451

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.206 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural basis of Src tyrosine kinase inhibition with a new class of potent and selective trisubstituted purine-based compounds.

Dalgarno, D.Stehle, T.Narula, S.Schelling, P.van Schravendijk, M.R.Adams, S.Andrade, L.Keats, J.Ram, M.Jin, L.Grossman, T.MacNeil, I.Metcalf III, C.Shakespeare, W.Wang, Y.Keenan, T.Sundaramoorthi, R.Bohacek, R.Weigele, M.Sawyer, T.

(2006) Chem Biol Drug Des 67: 46-57

  • DOI: https://doi.org/10.1111/j.1747-0285.2005.00316.x
  • Primary Citation of Related Structures:  
    2BDF, 2BDJ

  • PubMed Abstract: 

    The tyrosine kinase pp60src (Src) is the prototypical member of a family of proteins that participate in a broad array of cellular signal transduction processes, including cell growth, differentiation, survival, adhesion, and migration. Abnormal Src family kinase (SFK) signaling has been linked to several disease states, including osteoporosis and cancer metastases. Src has thus emerged as a molecular target for the discovery of small-molecule inhibitors that regulate Src kinase activity by binding to the ATP pocket within the catalytic domain. Here, we present crystal structures of the kinase domain of Src in complex with two purine-based inhibitors: AP23451, a small-molecule inhibitor designed to inhibit Src-dependent bone resorption, and AP23464, a small-molecule inhibitor designed to inhibit the Src-dependent metastatic spread of cancer. In each case, a trisubstituted purine template core was elaborated using structure-based drug design to yield a potent Src kinase inhibitor. These structures represent early examples of high affinity purine-based Src family kinase-inhibitor complexes, and they provide a detailed view of the specific protein-ligand interactions that lead to potent inhibition of Src. In particular, the 3-hydroxyphenethyl N9 substituent of AP23464 forms unique interactions with the protein that are critical to the picomolar affinity of this compound for Src. The comparison of these new structures with two relevant kinase-inhibitor complexes provides a structural basis for the observed kinase inhibitory selectivity. Further comparisons reveal a concerted induced-fit movement between the N- and C-terminal lobes of the kinase that correlates with the affinity of the ligand. Binding of the most potent inhibitor, AP23464, results in the largest induced-fit movement, which can be directly linked to interactions of the hydrophenethyl N9 substituent with a region at the interface between the two lobes. A less pronounced induced-fit movement is also observed in the Src-AP23451 complex. These new structures illustrate how the combination of structural, computational, and medicinal chemistry can be used to rationalize the process of developing high affinity, selective tyrosine kinase inhibitors as potential therapeutic agents.

  • Organizational Affiliation

    ARIAD Pharmaceuticals, 26 Landsdowne Street, Cambridge, MA 02139, USA. dalgarno@ariad.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src
A, B
279Homo sapiensMutation(s): 0 
Gene Names: SRCSRC1
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens)
Explore P12931 
Go to UniProtKB:  P12931
PHAROS:  P12931
GTEx:  ENSG00000197122 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12931
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 24A

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H28 N6 O5 P2
Binding Affinity Annotations 
IDSourceBinding Affinity
24A Binding MOAD:  2BDF IC50: 67 (nM) from 1 assay(s)
PDBBind:  2BDF IC50: 67 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.93α = 93.03
b = 59.74β = 91.43
c = 63.59γ = 97.79
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description