3K5V

Structure of Abl kinase in complex with imatinib and GNF-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors.

Zhang, J.Adrian, F.J.Jahnke, W.Cowan-Jacob, S.W.Li, A.G.Iacob, R.E.Sim, T.Powers, J.Dierks, C.Sun, F.Guo, G.R.Ding, Q.Okram, B.Choi, Y.Wojciechowski, A.Deng, X.Liu, G.Fendrich, G.Strauss, A.Vajpai, N.Grzesiek, S.Tuntland, T.Liu, Y.Bursulaya, B.Azam, M.Manley, P.W.Engen, J.R.Daley, G.Q.Warmuth, M.Gray, N.S.

(2010) Nature 463: 501-506

  • DOI: 10.1038/nature08675

  • PubMed Abstract: 
  • In an effort to find new pharmacological modalities to overcome resistance to ATP-binding-site inhibitors of Bcr-Abl, we recently reported the discovery of GNF-2, a selective allosteric Bcr-Abl inhibitor. Here, using solution NMR, X-ray crystallograp ...

    In an effort to find new pharmacological modalities to overcome resistance to ATP-binding-site inhibitors of Bcr-Abl, we recently reported the discovery of GNF-2, a selective allosteric Bcr-Abl inhibitor. Here, using solution NMR, X-ray crystallography, mutagenesis and hydrogen exchange mass spectrometry, we show that GNF-2 binds to the myristate-binding site of Abl, leading to changes in the structural dynamics of the ATP-binding site. GNF-5, an analogue of GNF-2 with improved pharmacokinetic properties, when used in combination with the ATP-competitive inhibitors imatinib or nilotinib, suppressed the emergence of resistance mutations in vitro, displayed additive inhibitory activity in biochemical and cellular assays against T315I mutant human Bcr-Abl and displayed in vivo efficacy against this recalcitrant mutant in a murine bone-marrow transplantation model. These results show that therapeutically relevant inhibition of Bcr-Abl activity can be achieved with inhibitors that bind to the myristate-binding site and that combining allosteric and ATP-competitive inhibitors can overcome resistance to either agent alone.


    Organizational Affiliation

    Dana-Farber Cancer Institute, Harvard Medical School, Department of Cancer Biology, Seeley G. Mudd Building 628, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ABL1
A, B
293Mus musculusMutation(s): 0 
Gene Names: Abl1 (Abl)
EC: 2.7.10.2
Find proteins for P00520 (Mus musculus)
Go to UniProtKB:  P00520
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
STJ
Query on STJ

Download SDF File 
Download CCD File 
A, B
3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)benzamide
C18 H13 F3 N4 O2
WEVYNIUIFUYDGI-UHFFFAOYSA-N
 Ligand Interaction
STI
Query on STI

Download SDF File 
Download CCD File 
A, B
4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
STI-571;IMATINIB
C29 H31 N7 O
KTUFNOKKBVMGRW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STJEC50: 140 nM (99) BINDINGDB
STJKd: 92 nM (99) BINDINGDB
STJIC50: 267 nM (99) BINDINGDB
STJKd: 500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.070α = 72.82
b = 65.268β = 80.25
c = 66.259γ = 84.86
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
MAR345data collection
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description