Crystal structure of human c-KIT kinase domain in complex with compound 15a

Experimental Data Snapshot

  • Resolution: 2.11 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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Identification of a Multitargeted Tyrosine Kinase Inhibitor for the Treatment of Gastrointestinal Stromal Tumors and Acute Myeloid Leukemia.

Lin, W.H.Wu, S.Y.Yeh, T.K.Chen, C.T.Song, J.S.Shiao, H.Y.Kuo, C.C.Hsu, T.Lu, C.T.Wang, P.C.Wu, T.S.Peng, Y.H.Lin, H.Y.Chen, C.P.Weng, Y.L.Kung, F.C.Wu, M.H.Su, Y.C.Huang, K.W.Chou, L.H.Hsueh, C.C.Yen, K.J.Kuo, P.C.Huang, C.L.Chen, L.T.Shih, C.Tsai, H.J.Jiaang, W.T.

(2019) J Med Chem 62: 11135-11150

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01229
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Gastrointestinal stromal tumors (GISTs) are prototypes of stem cell factor receptor (c-KIT)-driven cancer. Two receptor tyrosine kinases, c-KIT and fms-tyrosine kinase (FLT3), are frequently mutated in acute myeloid leukemia (AML) patients, and these mutations are associated with poor prognosis. In this study, we discovered a multitargeted tyrosine kinase inhibitor, compound 15a , with potent inhibition against single or double mutations of c-KIT developed in GISTs. Moreover, crystal structure analysis revealed the unique binding mode of 15a with c-KIT and may elucidate its high potency in inhibiting c-KIT kinase activity. Compound 15a inhibited cell proliferation and induced apoptosis by targeting c-KIT in c-KIT-mutant GIST cell lines. The antitumor effects of 15a were also demonstrated in GIST430 and GIST patient-derived xenograft models. Further studies demonstrated that 15a inhibited the proliferation of c-KIT- and FLT3-driven AML cells in vitro and in vivo. The results of this study suggest that 15a may be a potential anticancer drug for the treatment of GISTs and AML.

  • Organizational Affiliation

    Institute of Biotechnology and Pharmaceutical Research , National Health Research Institutes , No. 35, Keyan Road , Zhunan Town, Miaoli County 350 , Taiwan R.O.C.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit331Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DJX (Subject of Investigation/LOI)
Query on DJX

Download Ideal Coordinates CCD File 
B [auth A]N-[6-(4-ethylpiperazin-1-yl)-2-methyl-pyrimidin-4-yl]-5-pyridin-4-yl-1,3-thiazol-2-amine
C19 H23 N7 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.11 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.205α = 90
b = 63.205β = 90
c = 196.142γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description