6FEK

Oncogenic point mutation of RET receptor tyrosine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/s41467-018-02994-7
  • Primary Citation of Related Structures:  
    6FEK

  • 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 resulting in a serine-to-phenylalanine substitution at codon 904 in the activation loop of the RET kinase domain ...

    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

    Department of Thoracic Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa-city, Chiba, 2778577, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase receptor RetA299Homo sapiensMutation(s): 1 
Gene Names: RETCDHF12CDHR16PTCRET51
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens)
Explore P07949 
Go to UniProtKB:  P07949
PHAROS:  P07949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07949
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-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: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.901α = 90
b = 50.901β = 90
c = 242.515γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Francis Crick InstituteUnited KingdomFC001115

Revision History  (Full details and data files)

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