3OY3

Crystal structure of ABL T315I mutant kinase domain bound with a DFG-out inhibitor AP24589


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 

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
  • Primary Citation of Related Structures:  

  • 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 ABL1
A, B
284Mus musculusMutation(s): 1 
Gene Names: Abl1 (Abl)
EC: 2.7.10.2
Find proteins for P00520 (Mus musculus)
Go to UniProtKB:  P00520
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XY3
Query on XY3

Download SDF File 
Download CCD File 
A, B
5-[(5-{[4-{[4-(2-hydroxyethyl)piperazin-1-yl]methyl}-3-(trifluoromethyl)phenyl]carbamoyl}-2-methylphenyl)ethynyl]-1-methyl-1H-imidazole-2-carboxamide
C29 H31 F3 N6 O3
GOLRXYBFRBKBAG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XY3IC50: 3.6 nM (99) BINDINGDB
XY3IC50: 35.8 nM BINDINGMOAD
XY3IC50: 35.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.471α = 90.00
b = 59.988β = 97.97
c = 89.439γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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