3CS9 | pdb_00003cs9

Human ABL kinase in complex with nilotinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.242 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NILClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl

Weisberg, E.Manley, P.W.Breitenstein, W.Brueggen, J.Cowan-Jacob, S.W.Ray, A.Huntly, B.Fabbro, D.Fendrich, G.Hall-Meyers, E.Kung, A.L.Mestan, J.Daley, G.Q.Callahan, L.Catley, L.Cavazza, C.Azam, M.Neuberg, D.Wright, R.D.Gilliland, D.G.Griffin, J.D.

(2005) Cancer Cell 7: 129-141

  • DOI: https://doi.org/10.1016/j.ccr.2005.01.007
  • Primary Citation of Related Structures:  
    3CS9

  • PubMed Abstract: 

    The Bcr-Abl tyrosine kinase oncogene causes chronic myelogenous leukemia (CML) and Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL). We describe a novel selective inhibitor of Bcr-Abl, AMN107 (IC50 <30 nM), which is significantly more potent than imatinib, and active against a number of imatinib-resistant Bcr-Abl mutants. Crystallographic analysis of Abl-AMN107 complexes provides a structural explanation for the differential activity of AMN107 and imatinib against imatinib-resistant Bcr-Abl. Consistent with its in vitro and pharmacokinetic profile, AMN107 prolonged survival of mice injected with Bcr-Abl-transformed hematopoietic cell lines or primary marrow cells, and prolonged survival in imatinib-resistant CML mouse models. AMN107 is a promising new inhibitor for the therapy of CML and Ph+ ALL.


  • Organizational Affiliation

    Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase ABL1
A, B, C, D
277Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
PHAROS:  P00519
GTEx:  ENSG00000097007 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00519
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.242 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.926α = 90
b = 118.088β = 90
c = 123.683γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NILClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description