3OXZ

Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance.

Zhou, T.Commodore, L.Huang, W.S.Wang, Y.Thomas, M.Keats, J.Xu, Q.Rivera, V.M.Shakespeare, W.C.Clackson, T.Dalgarno, D.C.Zhu, X.

(2011) Chem Biol Drug Des 77: 1-11

  • DOI: 10.1111/j.1747-0285.2010.01054.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The BCR-ABL inhibitor imatinib has revolutionized the treatment of chronic myeloid leukemia. However, drug resistance caused by kinase domain mutations has necessitated the development of new mutation-resistant inhibitors, most recently against the T ...

    The BCR-ABL inhibitor imatinib has revolutionized the treatment of chronic myeloid leukemia. However, drug resistance caused by kinase domain mutations has necessitated the development of new mutation-resistant inhibitors, most recently against the T315I gatekeeper residue mutation. Ponatinib (AP24534) inhibits both native and mutant BCR-ABL, including T315I, acting as a pan-BCR-ABL inhibitor. Here, we undertook a combined crystallographic and structure-activity relationship analysis on ponatinib to understand this unique profile. While the ethynyl linker is a key inhibitor functionality that interacts with the gatekeeper, virtually all other components of ponatinib play an essential role in its T315I inhibitory activity. The extensive network of optimized molecular contacts found in the DFG-out binding mode leads to high potency and renders binding less susceptible to disruption by single point mutations. The inhibitory mechanism exemplified by ponatinib may have broad relevance to designing inhibitors against other kinases with mutated gatekeeper residues.


    Organizational Affiliation

    ARIAD Pharmaceuticals Inc., 26 Landsdowne Street, Cambridge, MA 02139, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ABL1A284Mus musculusMutation(s): 0 
Gene Names: Abl1Abl
EC: 2.7.10.2
Find proteins for P00520 (Mus musculus)
Explore P00520 
Go to UniProtKB:  P00520
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0LI
Query on 0LI

Download CCD File 
A
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide
C29 H27 F3 N6 O
PHXJVRSECIGDHY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0LIIC50:  7.699999809265137   nM  BindingDB
0LIIC50:  0.3700000047683716   nM  BindingDB
0LIEC50:  0.05000000074505806   nM  BindingDB
0LIKd:  0.699999988079071   nM  BindingDB
0LIIC50:  2.9000000953674316   nM  BindingDB
0LIIC50:  0.8999999761581421   nM  BindingDB
0LIIC50 :  8.600000381469727   nM  PDBBind
0LIIC50:  0.33000001311302185   nM  BindingDB
0LIIC50:  8.600000381469727   nM  BindingDB
0LIIC50:  1   nM  BindingDB
0LIEC50:  0.30000001192092896   nM  BindingDB
0LIIC50:  8.600000381469727   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.883α = 90
b = 59.906β = 96.01
c = 66.281γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-3000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance