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 

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Ligand Structure Quality Assessment 


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:  
    3OXZ, 3OY3

  • 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 T315I gatekeeper residue mutation ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1A284Mus musculusMutation(s): 0 
Gene Names: Abl1Abl
EC: 2.7.10.2
UniProt
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 (Subject of Investigation/LOI)
Query on 0LI

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
0LI BindingDB:  3OXZ Kd: 0.7 (nM) from 1 assay(s)
IC50: min: 0.31, max: 8.6 (nM) from 10 assay(s)
EC50: min: 0.05, max: 0.3 (nM) from 2 assay(s)
PDBBind:  3OXZ IC50: 8.6 (nM) from 1 assay(s)
Binding MOAD:  3OXZ IC50: 8.6 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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