Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.64 kDa 
• Atom Count: 2572 
• Modelled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 1

2F4J

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

• DOI: 10.2210/pdb2F4J/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-23 Released: 2006-01-24 
• Deposition Author(s): Young, M.A., Shah, N.P., Chao, L.H., Zarrinkar, P., Sawyers, P., Kuriyan, J.

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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 

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

• PubMed: 16424036 
• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase ABL1	A	287	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VX6	B [auth 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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
VX6	Kd:  3   nM  BindingDB
VX6	Kd:  9.300000190734863   nM  BindingDB
VX6	Kd:  5   nM  BindingDB
VX6	Kd:  45   nM  BindingDB
VX6	Ki:  42   nM  BindingDB
VX6	Kd:  100   nM  BindingDB
VX6	Ki:  30   nM  BindingDB
VX6	IC50:  320   nM  BindingDB
VX6	Kd:  480   nM  BindingDB
VX6	IC50:  420   nM  BindingDB
VX6	Kd:  7200   nM  BindingDB
VX6	Kd:  400   nM  BindingDB
VX6	Kd:  4   nM  BindingDB
VX6	Kd:  9.399999618530273   nM  BindingDB
VX6	Kd:  10   nM  BindingDB
VX6	Kd:  23   nM  BindingDB
VX6	IC50:  98   nM  BindingDB
VX6	Kd:  20   nM  BindingDB
VX6	Kd:  17   nM  BindingDB
VX6	IC50:  160   nM  BindingDB
VX6	Kd:  8   nM  BindingDB
VX6	Kd:  13   nM  BindingDB
VX6	Kd:  3.799999952316284   nM  BindingDB
VX6	IC50 :  2200   nM  PDBBind
VX6	Kd:  20   nM  BindingDB
VX6	Kd:  3.299999952316284   nM  BindingDB
VX6	Kd:  7.800000190734863   nM  BindingDB
VX6	Kd:  2100   nM  BindingDB
VX6	Kd:  9.100000381469727   nM  BindingDB
VX6	Kd:  7.5   nM  BindingDB
VX6	Kd:  7   nM  BindingDB
VX6	Kd:  6.300000190734863   nM  BindingDB
VX6	Kd:  3.0999999046325684   nM  BindingDB
VX6	Kd:  50   nM  BindingDB
VX6	Kd:  17000   nM  BindingDB
VX6	Kd:  5.300000190734863   nM  BindingDB
VX6	IC50:  50   nM  BindingDB
VX6	Kd:  6.300000190734863   nM  BindingDB
VX6	Kd:  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 = 44.768	α = 90
b = 59.417	β = 98.42
c = 66.896	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-23 
• Released Date: 2006-01-24 
Deposition Author(s): Young, M.A., Shah, N.P., Chao, L.H., Zarrinkar, P., Sawyers, P., Kuriyan, J.

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