3QTI

c-Met Kinase in Complex with NVP-BVU972


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Drug Resistance Screen Using a Selective MET Inhibitor Reveals a Spectrum of Mutations That Partially Overlap with Activating Mutations Found in Cancer Patients.

Tiedt, R.Degenkolbe, E.Furet, P.Appleton, B.A.Wagner, S.Schoepfer, J.Buck, E.Ruddy, D.A.Monahan, J.E.Jones, M.D.Blank, J.Haasen, D.Drueckes, P.Wartmann, M.McCarthy, C.Sellers, W.R.Hofmann, F.

(2011) Cancer Res 71: 5255-5264

  • DOI: 10.1158/0008-5472.CAN-10-4433
  • Primary Citation of Related Structures:  
    3QTI

  • PubMed Abstract: 
  • The emergence of drug resistance is a primary concern in any cancer treatment, including with targeted kinase inhibitors as exemplified by the appearance of Bcr-Abl point mutations in chronic myeloid leukemia (CML) patients treated with imatinib. In ...

    The emergence of drug resistance is a primary concern in any cancer treatment, including with targeted kinase inhibitors as exemplified by the appearance of Bcr-Abl point mutations in chronic myeloid leukemia (CML) patients treated with imatinib. In vitro approaches to identify resistance mutations in Bcr-Abl have yielded mutation spectra that faithfully recapitulated clinical observations. To predict resistance mutations in the receptor tyrosine kinase MET that could emerge during inhibitor treatment in patients, we conducted a resistance screen in BaF3 TPR-MET cells using the novel selective MET inhibitor NVP-BVU972. The observed spectrum of mutations in resistant cells was dominated by substitutions of tyrosine 1230 but also included other missense mutations and partially overlapped with activating MET mutations that were previously described in cancer patients. Cocrystallization of the MET kinase domain in complex with NVP-BVU972 revealed a key role for Y1230 in binding of NVP-BVU972, as previously reported for multiple other selective MET inhibitors. A second resistance screen in the same format with the MET inhibitor AMG 458 yielded a distinct spectrum of mutations rich in F1200 alterations, which is consistent with a different predicted binding mode. Our findings suggest that amino acid substitutions in the MET kinase domain of cancer patients need to be carefully monitored before and during treatment with MET inhibitors, as resistance may preexist or emerge. Compounds binding in the same manner as NVP-BVU972 might be particularly susceptible to the development of resistance through mutations in Y1230, a condition that may be addressed by MET inhibitors with alternative binding modes.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorAB314Homo sapiensMutation(s): 3 
Gene Names: MET
EC: 2.7.10.1
Find proteins for P08581 (Homo sapiens)
Explore P08581 
Go to UniProtKB:  P08581
NIH Common Fund Data Resources
PHAROS  P08581
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3QT
Query on 3QT

Download CCD File 
A, B
6-{[6-(1-methyl-1H-pyrazol-4-yl)imidazo[1,2-b]pyridazin-3-yl]methyl}quinoline
C20 H16 N6
RNCNPRCUHHDYPC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3QTIC50 :  14   nM  PDBBind
3QTIC50:  14   nM  BindingDB
3QTIC50:  14   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.69α = 103.94
b = 47.1β = 102.58
c = 81.2γ = 90.04
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-02-22 
  • Released Date: 2011-07-06 
  • Deposition Author(s): Appleton, B.A.

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-17
    Changes: Database references