3EFK

Structure of c-Met with pyrimidone inhibitor 50

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Design, synthesis, and biological evaluation of potent c-Met inhibitors.

D'Angelo, N.D., Bellon, S.F., Booker, S.K., Cheng, Y., Coxon, A., Dominguez, C., Fellows, I., Hoffman, D., Hungate, R., Kaplan-Lefko, P., Lee, M.R., Li, C., Liu, L., Rainbeau, E., Reider, P.J., Rex, K., Siegmund, A., Sun, Y., Tasker, A.S., Xi, N., Xu, S., Yang, Y., Zhang, Y., Burgess, T.L., Dussault, I., Kim, T.S.

(2008) J Med Chem 51: 5766-5779

  • DOI: 10.1021/jm8006189
  • Primary Citation of Related Structures:  
    3EFJ, 3EFK

  • PubMed Abstract: 

    • c-Met is a receptor tyrosine kinase that plays a key role in several cellular processes but has also been found to be overexpressed and mutated in different human cancers. Consequently, targeting this enzyme has become an area of intense research in ...

    c-Met is a receptor tyrosine kinase that plays a key role in several cellular processes but has also been found to be overexpressed and mutated in different human cancers. Consequently, targeting this enzyme has become an area of intense research in drug discovery. Our studies began with the design and synthesis of novel pyrimidone 7, which was found to be a potent c-Met inhibitor. Subsequent SAR studies identified 22 as a more potent analog, whereas an X-ray crystal structure of 7 bound to c-Met revealed an unexpected binding conformation. This latter finding led to the development of a new series that featured compounds that were more potent both in vitro and in vivo than 22 and also exhibited different binding conformations to c-Met. Novel c-Met inhibitors have been designed, developed, and found to be potent in vitro and in vivo.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799, USA. dangelo@amgen.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorA, B310Homo sapiensMutation(s): 1 
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
GTEx  ENSG00000105976
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MT4
Query on MT4
Download CCD File 
A, B
5-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-2-[(4-fluorophenyl)amino]-3-methylpyrimidin-4(3H)-one
C28 H22 F2 N4 O4
DUTNABYDBFVZOA-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MT4Ki:  14   nM  BindingDB
MT4Ki:  14   nM  Binding MOAD
MT4IC50:  14   nM  BindingDB
MT4Ki :  14   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.205α = 90
b = 78.25β = 90
c = 129.684γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance