PDBsum entry 3g0f

Transferase

PDB id: 3g0f

Contents

Protein chains

291 a.a. *

Ligands

B49 ×2

SO4

Waters ×15

* Residue conservation analysis

PDB id:

3g0f

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.

Resolution:

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

Date:

27-Jan-09 Release date: 24-Feb-09

Protein chains

P10721  (KIT_HUMAN) -  Mast/stem cell growth factor receptor Kit from Homo sapiens

Seq: 976 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.10.1 - receptor protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

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.

ABSTRACT

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.