Crystal structure of KIT1 in complex with DP2976 via co-crystallization

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 

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Ripretinib (DCC-2618) Is a Switch Control Kinase Inhibitor of a Broad Spectrum of Oncogenic and Drug-Resistant KIT and PDGFRA Variants.

Smith, B.D.Kaufman, M.D.Lu, W.P.Gupta, A.Leary, C.B.Wise, S.C.Rutkoski, T.J.Ahn, Y.M.Al-Ani, G.Bulfer, S.L.Caldwell, T.M.Chun, L.Ensinger, C.L.Hood, M.M.McKinley, A.Patt, W.C.Ruiz-Soto, R.Su, Y.Telikepalli, H.Town, A.Turner, B.A.Vogeti, L.Vogeti, S.Yates, K.Janku, F.Abdul Razak, A.R.Rosen, O.Heinrich, M.C.Flynn, D.L.

(2019) Cancer Cell 35: 738-751.e9

  • DOI: https://doi.org/10.1016/j.ccell.2019.04.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ripretinib (DCC-2618) was designed to inhibit the full spectrum of mutant KIT and PDGFRA kinases found in cancers and myeloproliferative neoplasms, particularly in gastrointestinal stromal tumors (GISTs), in which the heterogeneity of drug-resistant KIT mutations is a major challenge. Ripretinib is a "switch-control" kinase inhibitor that forces the activation loop (or activation "switch") into an inactive conformation. Ripretinib inhibits all tested KIT and PDGFRA mutants, and notably is a type II kinase inhibitor demonstrated to broadly inhibit activation loop mutations in KIT and PDGFRA, previously thought only achievable with type I inhibitors. Ripretinib shows efficacy in preclinical cancer models, and preliminary clinical data provide proof-of-concept that ripretinib inhibits a wide range of KIT mutants in patients with drug-resistant GISTs.

  • Organizational Affiliation

    Deciphera Pharmaceuticals, Inc., Waltham, MA 02451, USA. Electronic address: dflynn@deciphera.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit312Homo sapiensMutation(s): 0 
Gene Names: KITSCFR
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
PHAROS:  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
JWY (Subject of Investigation/LOI)
Query on JWY

Download Ideal Coordinates CCD File 
P [auth A]N-{4-chloro-5-[1-ethyl-7-(methylamino)-2-oxo-1,2-dihydro-1,6-naphthyridin-3-yl]-2-fluorophenyl}-N'-phenylurea
C24 H21 Cl F N5 O2
Query on NO3

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.699α = 90
b = 80.699β = 90
c = 145.02γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release