6FEK

Oncogenic point mutation of RET receptor tyrosine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A secondary RET mutation in the activation loop conferring resistance to vandetanib.

Nakaoku, T.Kohno, T.Araki, M.Niho, S.Chauhan, R.Knowles, P.P.Tsuchihara, K.Matsumoto, S.Shimada, Y.Mimaki, S.Ishii, G.Ichikawa, H.Nagatoishi, S.Tsumoto, K.Okuno, Y.Yoh, K.McDonald, N.Q.Goto, K.

(2018) Nat Commun 9: 625-625

  • DOI: 10.1038/s41467-018-02994-7

  • PubMed Abstract: 
  • Resistance to vandetanib, a type I RET kinase inhibitor, developed in a patient with metastatic lung adenocarcinoma harboring a CCDC6-RET fusion that initially exhibited a response to treatment. The resistant tumor acquired a secondary mutation resul ...

    Resistance to vandetanib, a type I RET kinase inhibitor, developed in a patient with metastatic lung adenocarcinoma harboring a CCDC6-RET fusion that initially exhibited a response to treatment. The resistant tumor acquired a secondary mutation resulting in a serine-to-phenylalanine substitution at codon 904 in the activation loop of the RET kinase domain. The S904F mutation confers resistance to vandetanib by increasing the ATP affinity and autophosphorylation activity of RET kinase. A reduced interaction with the drug is also observed in vitro for the S904F mutant by thermal shift assay. A crystal structure of the S904F mutant reveals a small hydrophobic core around F904 likely to enhance basal kinase activity by stabilizing an active conformer. Our findings indicate that missense mutations in the activation loop of the kinase domain are able to increase kinase activity and confer drug resistance through allosteric effects.


    Organizational Affiliation

    Signaling and Structural Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shiroganedai, Minato-ku, Tokyo, 1088639, Japan.,Division of Genome Biology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan.,Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, 54 Kawaracho, Shogoin, Kyoto-city, Kyoto, 6068507, Japan.,Department of Thoracic Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa-city, Chiba, 2778577, Japan.,Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1, Kashiwanoha, Kashiwa-City, Chiba, 2778577, Japan.,Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.,Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe-city, Hyogo, 6500047, Japan.,Division of Genome Biology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan. tkkohno@ncc.go.jp.,Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 1040045, Japan. tkkohno@ncc.go.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase receptor Ret
A
299Homo sapiensMutation(s): 1 
Gene Names: RET (CDHF12, CDHR16, PTC, RET51)
EC: 2.7.10.1
Find proteins for P07949 (Homo sapiens)
Go to Gene View: RET
Go to UniProtKB:  P07949
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
A
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 50.901α = 90.00
b = 50.901β = 90.00
c = 242.515γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Francis Crick InstituteUnited KingdomFC001115

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection