2F4J

Structure of the Kinase Domain of an Imatinib-Resistant Abl Mutant in Complex with the Aurora Kinase Inhibitor VX-680

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680.

Young, M.A., Shah, N.P., Chao, L.H., Seeliger, M., Milanov, Z.V., Biggs, W.H., Treiber, D.K., Patel, H.K., Zarrinkar, P.P., Lockhart, D.J., Sawyers, C.L., Kuriyan, J.

(2006) Cancer Res 66: 1007-1014

  • DOI: 10.1158/0008-5472.CAN-05-2788
  • Primary Citation of Related Structures:  
    2F4J

  • PubMed Abstract: 

    • We present a high-resolution (2.0 A) crystal structure of the catalytic domain of a mutant form of the Abl tyrosine kinase (H396P; Abl-1a numbering) that is resistant to the Abl inhibitor imatinib. The structure is determined in complex with the smal ...

    We present a high-resolution (2.0 A) crystal structure of the catalytic domain of a mutant form of the Abl tyrosine kinase (H396P; Abl-1a numbering) that is resistant to the Abl inhibitor imatinib. The structure is determined in complex with the small-molecule inhibitor VX-680 (Vertex Pharmaceuticals, Cambridge, MA), which blocks the activity of various imatinib-resistant mutant forms of Abl, including one (T315I) that is resistant to both imatinib and BMS-354825 (dasatinib), a dual Src/Abl inhibitor that seems to be clinically effective against all other imatinib-resistant forms of BCR-Abl. VX-680 is shown to have significant inhibitory activity against BCR-Abl bearing the T315I mutation in patient-derived samples. The Abl kinase domain bound to VX-680 is not phosphorylated on the activation loop in the crystal structure but is nevertheless in an active conformation, previously unobserved for Abl and inconsistent with the binding of imatinib. The adoption of an active conformation is most likely the result of synergy between the His(396)Pro mutation, which destabilizes the inactive conformation required for imatinib binding, and the binding of VX-680, which favors the active conformation through hydrogen bonding and steric effects. VX-680 is bound to Abl in a mode that accommodates the substitution of isoleucine for threonine at residue 315 (the "gatekeeper" position). The avoidance of the innermost cavity of the Abl kinase domain by VX-680 and the specific recognition of the active conformation explain the effectiveness of this compound against mutant forms of BCR-Abl, including those with mutations at the gatekeeper position.

    Organizational Affiliation: 

    Departments of Molecular and Cell Biology and Chemistry, Howard Hughes Medical Institute, The University of California at Berkeley, Berkeley, CA 94720, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase ABL1A287Homo sapiensMutation(s): 1 
Gene Names: ABL1, ABL, JTK7
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS  P00519
GTEx  ENSG00000097007
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VX6
Query on VX6
Download Ideal Coordinates CCD File 
A
CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE
C23 H28 N8 O S
GCIKSSRWRFVXBI-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VX6Kd:  3   nM  BindingDB
VX6Kd:  9.300000190734863   nM  BindingDB
VX6Kd:  5   nM  BindingDB
VX6Kd:  45   nM  BindingDB
VX6Ki:  42   nM  BindingDB
VX6Kd:  100   nM  BindingDB
VX6Ki:  30   nM  BindingDB
VX6IC50:  320   nM  BindingDB
VX6Kd:  480   nM  BindingDB
VX6IC50:  420   nM  BindingDB
VX6Kd:  7200   nM  BindingDB
VX6Kd:  400   nM  BindingDB
VX6Kd:  4   nM  BindingDB
VX6Kd:  9.399999618530273   nM  BindingDB
VX6Kd:  10   nM  BindingDB
VX6Kd:  23   nM  BindingDB
VX6IC50:  98   nM  BindingDB
VX6Kd:  20   nM  BindingDB
VX6Kd:  17   nM  BindingDB
VX6IC50:  160   nM  BindingDB
VX6Kd:  8   nM  BindingDB
VX6Kd:  13   nM  BindingDB
VX6Kd:  3.799999952316284   nM  BindingDB
VX6IC50 :  2200   nM  PDBBind
VX6Kd:  20   nM  BindingDB
VX6Kd:  3.299999952316284   nM  BindingDB
VX6Kd:  7.800000190734863   nM  BindingDB
VX6Kd:  2100   nM  BindingDB
VX6Kd:  9.100000381469727   nM  BindingDB
VX6Kd:  7.5   nM  BindingDB
VX6Kd:  7   nM  BindingDB
VX6Kd:  6.300000190734863   nM  BindingDB
VX6Kd:  3.0999999046325684   nM  BindingDB
VX6Kd:  50   nM  BindingDB
VX6Kd:  17000   nM  BindingDB
VX6Kd:  5.300000190734863   nM  BindingDB
VX6Kd:  6.300000190734863   nM  BindingDB
VX6Kd:  9.699999809265137   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.768α = 90
b = 59.417β = 98.42
c = 66.896γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    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: 2017-10-18
    Changes: Refinement description