Crystal structure of KIT in complex with ponatinib

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 

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This is version 1.3 of the entry. See complete history


Ponatinib Inhibits Polyclonal Drug-Resistant KIT Oncoproteins and Shows Therapeutic Potential in Heavily Pretreated Gastrointestinal Stromal Tumor (GIST) Patients.

Garner, A.P.Gozgit, J.M.Anjum, R.Vodala, S.Schrock, A.Zhou, T.Serrano, C.Eilers, G.Zhu, M.Ketzer, J.Wardwell, S.Ning, Y.Song, Y.Kohlmann, A.Wang, F.Clackson, T.Heinrich, M.C.Fletcher, J.A.Bauer, S.Rivera, V.M.

(2014) Clin Cancer Res 20: 5745-5755

  • DOI: https://doi.org/10.1158/1078-0432.CCR-14-1397
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    KIT is the major oncogenic driver of gastrointestinal stromal tumors (GIST). Imatinib, sunitinib, and regorafenib are approved therapies; however, efficacy is often limited by the acquisition of polyclonal secondary resistance mutations in KIT, with those located in the activation (A) loop (exons 17/18) being particularly problematic. Here, we explore the KIT-inhibitory activity of ponatinib in preclinical models and describe initial characterization of its activity in patients with GIST.

  • Organizational Affiliation

    ARIAD Pharmaceuticals, Inc, Cambridge, MA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit315Homo sapiensMutation(s): 0 
Gene Names: KITSCFR
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
GTEx:  ENSG00000157404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10721
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
O4 P
Binding Affinity Annotations 
IDSourceBinding Affinity
0LI Binding MOAD:  4U0I IC50: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.032α = 90
b = 70.032β = 90
c = 129.212γ = 120
Software Package:
Software NamePurpose
StructureStudiodata collection
HKL-2000data scaling
Quantamodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary