1IEP

CRYSTAL STRUCTURE OF THE C-ABL KINASE DOMAIN IN COMPLEX WITH STI-571.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.R.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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABLA, B293Mus musculusMutation(s): 0 
Gene Names: Abl1Abl
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P00520 (Mus musculus)
Explore P00520 
Go to UniProtKB:  P00520
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STI
Query on STI

Download Ideal Coordinates CCD File 
G [auth A], J [auth B]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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STIIC50:  300   nM  BindingDB
STIIC50:  319   nM  BindingDB
STIKd:  10000   nM  BindingDB
STIIC50:  340   nM  BindingDB
STIIC50:  250   nM  BindingDB
STIKd:  13   nM  BindingDB
STIKd:  35   nM  BindingDB
STIIC50 :  100   nM  PDBBind
STIKd:  20   nM  BindingDB
STIIC50:  430   nM  BindingDB
STIIC50:  436   nM  BindingDB
STIKd:  21   nM  BindingDB
STIEC50:  1000   nM  BindingDB
STIKd:  6000   nM  BindingDB
STIKd:  24   nM  BindingDB
STIKd:  6200   nM  BindingDB
STIIC50:  372   nM  BindingDB
STIIC50:  399   nM  BindingDB
STIKd:  60   nM  BindingDB
STIIC50:  658   nM  BindingDB
STIIC50:  678   nM  BindingDB
STIIC50:  682   nM  BindingDB
STIKd:  62   nM  BindingDB
STIIC50:  470   nM  BindingDB
STIIC50:  473   nM  BindingDB
STIIC50:  1000   nM  BindingDB
STIKd:  65   nM  BindingDB
STIKd:  77   nM  BindingDB
STIKd:  40   nM  BindingDB
STIIC50:  1.100000023841858   nM  BindingDB
STIIC50:  40   nM  BindingDB
STIKd:  44   nM  BindingDB
STIKd:  1.100000023841858   nM  BindingDB
STIKd:  1.7999999523162842   nM  BindingDB
STIIC50:  750   nM  BindingDB
STIIC50:  74   nM  BindingDB
STIIC50:  730   nM  BindingDB
STIKd:  130   nM  BindingDB
STIIC50:  110   nM  BindingDB
STIIC50:  116   nM  BindingDB
STIKd:  92   nM  BindingDB
STIKd:  100   nM  BindingDB
STIIC50:  98   nM  BindingDB
STIKd:  110   nM  BindingDB
STIEC50:  34   nM  BindingDB
STIKi:  13   nM  BindingDB
STIIC50:  170   nM  BindingDB
STIIC50:  204   nM  BindingDB
STIKd:  170   nM  BindingDB
STIIC50:  221   nM  BindingDB
STIIC50:  223   nM  BindingDB
STIIC50:  234   nM  BindingDB
STIKi:  14   nM  BindingDB
STIIC50:  188   nM  BindingDB
STIIC50:  190   nM  BindingDB
STIIC50:  194   nM  BindingDB
STIIC50:  200   nM  BindingDB
STIKd:  10   nM  BindingDB
STIKi:  7000   nM  BindingDB
STIIC50:  20   nM  BindingDB
STIKd:  5.900000095367432   nM  BindingDB
STIEC50:  70   nM  BindingDB
STIIC50:  100   nM  Binding MOAD
STIKd:  2   nM  BindingDB
STIKd:  580   nM  BindingDB
STIEC50:  90   nM  BindingDB
STIIC50:  5000   nM  BindingDB
STIIC50:  27   nM  BindingDB
STIIC50:  1000   nM  BindingDB
STIKi:  37   nM  BindingDB
STIKd:  1.5   nM  BindingDB
STIKd:  8.300000190734863   nM  BindingDB
STIIC50:  38   nM  BindingDB
STIIC50:  40   nM  BindingDB
STIIC50:  8600   nM  BindingDB
STIKd:  2.5   nM  BindingDB
STIKd:  8.5   nM  BindingDB
STIIC50:  1100   nM  BindingDB
STIIC50:  10.800000190734863   nM  BindingDB
STIIC50:  1200   nM  BindingDB
STIKd:  2.200000047683716   nM  BindingDB
STIIC50:  272   nM  BindingDB
STIKd:  14   nM  BindingDB
STIIC50:  2700   nM  BindingDB
STIIC50:  1900   nM  BindingDB
STIKd:  1   nM  BindingDB
STIIC50:  13   nM  BindingDB
STIKd:  10   nM  BindingDB
STIIC50:  14   nM  BindingDB
STIKi:  298   nM  BindingDB
STIKd:  12   nM  BindingDB
STIIC50:  3100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.885α = 90
b = 147.371β = 90
c = 153.442γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance