Crystal Structure of the c-Abl Kinase domain in complex with PD173955

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 

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Crystal Structures of the Kinase Domain of c-Abl in Complex with the Small Molecule Inhibitors PD173955 and Imatinib (STI-571)

Nagar, B.Bornmann, W.Pellicena, P.Schindler, T.Veach, D.Miller, W.T.Clarkson, B.Kuriyan, J.

(2002) Cancer Res 62: 4236-4243

  • Primary Citation of Related Structures:  
    1IEP, 1M52

  • PubMed Abstract: 

    The inadvertent fusion of the bcr gene with the abl gene results in a constitutively active tyrosine kinase (Bcr-Abl) that transforms cells and causes chronic myelogenous leukemia. Small molecule inhibitors of Bcr-Abl that bind to the kinase domain can be used to treat chronic myelogenous leukemia. We report crystal structures of the kinase domain of Abl in complex with two such inhibitors, imatinib (also known as STI-571 and Gleevec) and PD173955 (Parke-Davis). Both compounds bind to the canonical ATP-binding site of the kinase domain, but they do so in different ways. As shown previously in a crystal structure of Abl bound to a smaller variant of STI-571, STI-571 captures a specific inactive conformation of the activation loop of Abl in which the loop mimics bound peptide substrate. In contrast, PD173955 binds to a conformation of Abl in which the activation loop resembles that of an active kinase. The structure suggests that PD173955 would be insensitive to whether the conformation of the activation loop corresponds to active kinases or to that seen in the STI-571 complex. In vitro kinase assays confirm that this is the case and indicate that PD173955 is at least 10-fold more inhibitory than STI-571. The structures suggest that PD173955 achieves its greater potency over STI-571 by being able to target multiple forms of Abl (active or inactive), whereas STI-571 requires a specific inactive conformation of Abl.

  • Organizational Affiliation

    Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
293Mus musculusMutation(s): 0 
Find proteins for P00520 (Mus musculus)
Explore P00520 
Go to UniProtKB:  P00520
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00520
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P17

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
C21 H16 Cl2 N4 O S
Query on MES

Download Ideal Coordinates CCD File 
D [auth B],
E [auth B]
C6 H13 N O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
P17 BindingDB:  1M52 Ki: 0.2 (nM) from 1 assay(s)
Kd: min: 0.52, max: 2100 (nM) from 16 assay(s)
IC50: min: 2, max: 28 (nM) from 4 assay(s)
EC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.848α = 90
b = 125.708β = 90
c = 56.718γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description