PDBsum entry 3g0f

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Transferase PDB id
Protein chains
291 a.a. *
B49 ×2
Waters ×15
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Kit kinase domain mutant d816h in complex with sunitinib
Structure: Mast/stem cell growth factor receptor. Chain: a, b. Fragment: kinase domain - kid deleted. Synonym: scfr, proto-oncogene tyrosine-protein kinase kit, c-kit. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: kit. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
2.60Å     R-factor:   0.207     R-free:   0.255
Authors: K.S.Gajiwala,J.C.Wu,E.A.Lunney,G.D.Demetri
Key ref:
K.S.Gajiwala et al. (2009). KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients. Proc Natl Acad Sci U S A, 106, 1542-1547. PubMed id: 19164557 DOI: 10.1073/pnas.0812413106
27-Jan-09     Release date:   24-Feb-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P10721  (KIT_HUMAN) -  Mast/stem cell growth factor receptor Kit
976 a.a.
291 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Receptor protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Bound ligand (Het Group name = B49)
matches with 44.00% similarity
+ [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     transmembrane receptor protein tyrosine kinase signaling pathway   2 terms 
  Biochemical function     transferase activity, transferring phosphorus-containing groups     5 terms  


DOI no: 10.1073/pnas.0812413106 Proc Natl Acad Sci U S A 106:1542-1547 (2009)
PubMed id: 19164557  
KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients.
K.S.Gajiwala, J.C.Wu, J.Christensen, G.D.Deshmukh, W.Diehl, J.P.Dinitto, J.M.English, M.J.Greig, Y.A.He, S.L.Jacques, E.A.Lunney, M.McTigue, D.Molina, T.Quenzer, P.A.Wells, X.Yu, Y.Zhang, A.Zou, M.R.Emmett, A.G.Marshall, H.M.Zhang, G.D.Demetri.
Most gastrointestinal stromal tumors (GISTs) exhibit aberrant activation of the receptor tyrosine kinase (RTK) KIT. The efficacy of the inhibitors imatinib mesylate and sunitinib malate in GIST patients has been linked to their inhibition of these mutant KIT proteins. However, patients on imatinib can acquire secondary KIT mutations that render the protein insensitive to the inhibitor. Sunitinib has shown efficacy against certain imatinib-resistant mutants, although a subset that resides in the activation loop, including D816H/V, remains resistant. Biochemical and structural studies were undertaken to determine the molecular basis of sunitinib resistance. Our results show that sunitinib targets the autoinhibited conformation of WT KIT and that the D816H mutant undergoes a shift in conformational equilibrium toward the active state. These findings provide a structural and enzymologic explanation for the resistance profile observed with the KIT inhibitors. Prospectively, they have implications for understanding oncogenic kinase mutants and for circumventing drug resistance.
  Selected figure(s)  
Figure 1.
Overview of the KIT gene and protein. (A) Schematic representation of KIT showing location of functional domains, primary (1°) and secondary (2°) mutations (mut.). Frequencies of primary KIT genotypes, specific secondary KIT mutations, and resistance (R) or sensitivity (S) to imatinib (IM) or sunitinib (SU) were those reported in a phase I/II trial of sunitinib in advanced GIST after imatinib failure (6). V560D, substitution of Asp for Val at residue 560. (B) The unactivated, autoinhibited and activated forms of WT KIT (7, 8). The JM domain (red), A-loop (green), and C α-helix (cyan) are oriented differently in the autoinhibited and activated states. *V560D generally occurs as a primary mutation.
Figure 3.
Sunitinib recognizes the autoinhibited form of KIT. WT KIT bound to sunitinib is shown in yellow (JM domain, red; A-loop, green; C α-helix, cyan). (A) WT KIT bound to sunitinib is very similar to the published autoinhibited structure of KIT (gray) (7, 8). Amino acid side chains are shown at the sites of A-loop substitutions found in sunitinib-resistant GISTs. (B) Sunitinib-binding site in the complex and apo structures. Drug binding induces a slight rearrangement of the Phe-811 side chain relative to the apo form. (C) The overall structure of the D816H mutant bound to sunitinib (darker blue) is very similar to that with WT, except for the proposed dislocation of the JM domain from its autoinhibitory position. Residue 816 is shown for both proteins.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22089421 C.L.Corless, C.M.Barnett, and M.C.Heinrich (2011).
Gastrointestinal stromal tumours: origin and molecular oncology.
  Nat Rev Cancer, 11, 865-878.  
21419931 G.D.Demetri (2011).
Differential properties of current tyrosine kinase inhibitors in gastrointestinal stromal tumors.
  Semin Oncol, 38, S10-S19.  
21429632 H.M.Shallal, and W.A.Russu (2011).
Discovery, synthesis, and investigation of the antitumor activity of novel piperazinylpyrimidine derivatives.
  Eur J Med Chem, 46, 2043-2057.  
21319869 K.N.Ganjoo, and S.Patel (2011).
Current and emerging pharmacological treatments for gastrointestinal stromal tumour.
  Drugs, 71, 321-330.  
21364689 M.A.Pierotti, E.Tamborini, T.Negri, S.Pricl, and S.Pilotti (2011).
Targeted therapy in GIST: in silico modeling for prediction of resistance.
  Nat Rev Clin Oncol, 8, 161-170.  
  21528013 M.J.Chalmers, B.D.Pascal, S.Willis, J.Zhang, S.J.Iturria, J.A.Dodge, and P.R.Griffin (2011).
Methods for the Analysis of High Precision Differential Hydrogen Deuterium Exchange Data.
  Int J Mass Spectrom, 302, 59-68.  
21329427 M.J.Chalmers, S.A.Busby, B.D.Pascal, G.M.West, and P.R.Griffin (2011).
Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions.
  Expert Rev Proteomics, 8, 43-59.  
20673774 R.E.Hubbard (2011).
Structure-based drug discovery and protein targets in the CNS.
  Neuropharmacology, 60, 7.  
21481795 W.W.Chan, S.C.Wise, M.D.Kaufman, Y.M.Ahn, C.L.Ensinger, T.Haack, M.M.Hood, J.Jones, J.W.Lord, W.P.Lu, D.Miller, W.C.Patt, B.D.Smith, P.A.Petillo, T.J.Rutkoski, H.Telikepalli, L.Vogeti, T.Yao, L.Chun, R.Clark, P.Evangelista, L.C.Gavrilescu, K.Lazarides, V.M.Zaleskas, L.J.Stewart, R.A.Van Etten, and D.L.Flynn (2011).
Conformational control inhibition of the BCR-ABL1 tyrosine kinase, including the gatekeeper T315I mutant, by the switch-control inhibitor DCC-2036.
  Cancer Cell, 19, 556-568.
PDB codes: 3qri 3qrj 3qrk
20108972 A.A.Edwards, J.D.Tipton, M.D.Brenowitz, M.R.Emmett, A.G.Marshall, G.B.Evans, P.C.Tyler, and V.L.Schramm (2010).
Conformational states of human purine nucleoside phosphorylase at rest, at work, and with transition state analogues.
  Biochemistry, 49, 2058-2067.  
20890793 A.Tsujimura, H.Kiyoi, Y.Shiotsu, Y.Ishikawa, Y.Mori, H.Ishida, T.Toki, E.Ito, and T.Naoe (2010).
Selective KIT inhibitor KI-328 and HSP90 inhibitor show different potency against the type of KIT mutations recurrently identified in acute myeloid leukemia.
  Int J Hematol, 92, 624-633.  
20690803 A.Wozniak, G.Floris, M.Debiec-Rychter, R.Sciot, and P.Schöffski (2010).
Implications of mutational analysis for the management of patients with gastrointestinal stromal tumors and the application of targeted therapies.
  Cancer Invest, 28, 839-848.  
20398925 H.I.Scher, T.M.Beer, C.S.Higano, A.Anand, M.E.Taplin, E.Efstathiou, D.Rathkopf, J.Shelkey, E.Y.Yu, J.Alumkal, D.Hung, M.Hirmand, L.Seely, M.J.Morris, D.C.Danila, J.Humm, S.Larson, M.Fleisher, and C.L.Sawyers (2010).
Antitumour activity of MDV3100 in castration-resistant prostate cancer: a phase 1-2 study.
  Lancet, 375, 1437-1446.  
20099838 H.M.Zhang, S.M.McLoughlin, S.D.Frausto, H.Tang, M.R.Emmett, and A.G.Marshall (2010).
Simultaneous reduction and digestion of proteins with disulfide bonds for hydrogen/deuterium exchange monitored by mass spectrometry.
  Anal Chem, 82, 1450-1454.  
20095048 H.M.Zhang, X.Yu, M.J.Greig, K.S.Gajiwala, J.C.Wu, W.Diehl, E.A.Lunney, M.R.Emmett, and A.G.Marshall (2010).
Drug binding and resistance mechanism of KIT tyrosine kinase revealed by hydrogen/deuterium exchange FTICR mass spectrometry.
  Protein Sci, 19, 703-715.  
20947481 J.Martín-Broto, L.Rubio, R.Alemany, and J.A.López-Guerrero (2010).
Clinical implications of KIT and PDGFRA genotyping in GIST.
  Clin Transl Oncol, 12, 670-676.  
20147452 J.P.DiNitto, G.D.Deshmukh, Y.Zhang, S.L.Jacques, R.Coli, J.W.Worrall, W.Diehl, J.M.English, and J.C.Wu (2010).
Function of activation loop tyrosine phosphorylation in the mechanism of c-Kit auto-activation and its implication in sunitinib resistance.
  J Biochem, 147, 601-609.  
20012482 K.J.Gotink, and H.M.Verheul (2010).
Anti-angiogenic tyrosine kinase inhibitors: what is their mechanism of action?
  Angiogenesis, 13, 1.  
21095574 L.M.Wodicka, P.Ciceri, M.I.Davis, J.P.Hunt, M.Floyd, S.Salerno, X.H.Hua, J.M.Ford, R.C.Armstrong, P.P.Zarrinkar, and D.K.Treiber (2010).
Activation state-dependent binding of small molecule kinase inhibitors: structural insights from biochemistry.
  Chem Biol, 17, 1241-1249.  
20361266 P.A.Cassier, and J.Y.Blay (2010).
Molecular response prediction in gastrointestinal stromal tumors.
  Target Oncol, 5, 29-37.  
  20161982 R.Quek, and S.George (2010).
Update on the treatment of gastrointestinal stromal tumors (GISTs): role of imatinib.
  Biologics, 4, 19-31.  
20140688 R.Rajasekaran, and R.Sethumadhavan (2010).
Exploring the cause of drug resistance by the detrimental missense mutations in KIT receptor: computational approach.
  Amino Acids, 39, 651-660.  
  20633291 S.Caenepeel, L.Renshaw-Gegg, A.Baher, T.L.Bush, W.Baron, T.Juan, R.Manoukian, A.S.Tasker, A.Polverino, and P.E.Hughes (2010).
Motesanib inhibits Kit mutations associated with gastrointestinal stromal tumors.
  J Exp Clin Cancer Res, 29, 96.  
20116280 S.Kazazic, H.M.Zhang, T.M.Schaub, M.R.Emmett, C.L.Hendrickson, G.T.Blakney, and A.G.Marshall (2010).
Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry.
  J Am Soc Mass Spectrom, 21, 550-558.  
20385359 S.Liu, L.C.Wu, J.Pang, R.Santhanam, S.Schwind, Y.Z.Wu, C.J.Hickey, J.Yu, H.Becker, K.Maharry, M.D.Radmacher, C.Li, S.P.Whitman, A.Mishra, N.Stauffer, A.M.Eiring, R.Briesewitz, R.A.Baiocchi, K.K.Chan, P.Paschka, M.A.Caligiuri, J.C.Byrd, C.M.Croce, C.D.Bloomfield, D.Perrotti, R.Garzon, and G.Marcucci (2010).
Sp1/NFkappaB/HDAC/miR-29b regulatory network in KIT-driven myeloid leukemia.
  Cancer Cell, 17, 333-347.  
19467916 E.Weisberg, R.Barrett, Q.Liu, R.Stone, N.Gray, and J.D.Griffin (2009).
FLT3 inhibition and mechanisms of drug resistance in mutant FLT3-positive AML.
  Drug Resist Updat, 12, 81-89.  
19648052 H.J.Broxterman, K.J.Gotink, and H.M.Verheul (2009).
Understanding the causes of multidrug resistance in cancer: a comparison of doxorubicin and sunitinib.
  Drug Resist Updat, 12, 114-126.  
19788312 J.R.Engen (2009).
Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS.
  Anal Chem, 81, 7870-7875.  
19861442 T.Guo, M.Hajdu, N.P.Agaram, H.Shinoda, D.Veach, B.D.Clarkson, R.G.Maki, S.Singer, R.P.Dematteo, P.Besmer, and C.R.Antonescu (2009).
Mechanisms of sunitinib resistance in gastrointestinal stromal tumors harboring KITAY502-3ins mutation: an in vitro mutagenesis screen for drug resistance.
  Clin Cancer Res, 15, 6862-6870.  
20047122 T.Nishida, T.Takahashi, and Y.Miyazaki (2009).
Gastrointestinal stromal tumor: a bridge between bench and bedside.
  Gastric Cancer, 12, 175-188.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.