2HYY

Human Abl kinase domain in complex with imatinib (STI571, Glivec)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia.

Cowan-Jacob, S.W.Fendrich, G.Floersheimer, A.Furet, P.Liebetanz, J.Rummel, G.Rheinberger, P.Centeleghe, M.Fabbro, D.Manley, P.W.

(2007) Acta Crystallogr D Biol Crystallogr 63: 80-93

  • DOI: 10.1107/S0907444906047287
  • Primary Citation of Related Structures:  
    2HYY, 2HZ4, 2HZ0, 2HZI, 2HZN

  • PubMed Abstract: 
  • Chronic myelogenous leukaemia (CML) results from the Bcr-Abl oncoprotein, which has a constitutively activated Abl tyrosine kinase domain. Although most chronic phase CML patients treated with imatinib as first-line therapy maintain excellent durable ...

    Chronic myelogenous leukaemia (CML) results from the Bcr-Abl oncoprotein, which has a constitutively activated Abl tyrosine kinase domain. Although most chronic phase CML patients treated with imatinib as first-line therapy maintain excellent durable responses, patients who have progressed to advanced-stage CML frequently fail to respond or lose their response to therapy owing to the emergence of drug-resistant mutants of the protein. More than 40 such point mutations have been observed in imatinib-resistant patients. The crystal structures of wild-type and mutant Abl kinase in complex with imatinib and other small-molecule Abl inhibitors were determined, with the aim of understanding the molecular basis of resistance and to aid in the design and optimization of inhibitors active against the resistance mutants. These results are presented in a way which illustrates the approaches used to generate multiple structures, the type of information that can be gained and the way that this information is used to support drug discovery.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, Basel, Switzerland. sandra.jacob@novartis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase ABL1A, B, C, D273Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS  P00519
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STI
Query on STI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.679α = 90
b = 148.575β = 90
c = 115.217γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-16
    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: 2017-10-18
    Changes: Refinement description