Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.73 kDa 
• Atom Count: 4486 
• Modelled Residue Count: 548 
• Deposited Residue Count: 620 
• Unique protein chains: 1

3EFK

Structure of c-Met with pyrimidone inhibitor 50

• PDB DOI: 10.2210/pdb3EFK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2008-09-09 Released: 2008-10-07 
• Deposition Author(s): Bellon, S.F., D'Angelo, N., Whittington, D., Dussault, I.

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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 

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

• PubMed: 18763753 
• 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 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A, B	310	Homo sapiens	Mutation(s): 1  Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
PHAROS:  P08581

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MT4	C [auth A], D [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
MT4	PDBBind:  3EFK	Ki: 14 (nM) from 1 assay(s)
	BindingDB:  3EFK	Ki: 14 (nM) from 1 assay(s)
		IC50: 14 (nM) from 1 assay(s)
	Binding MOAD:  3EFK	Ki: 14 (nM) from 1 assay(s)

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 = 76.205	α = 90
b = 78.25	β = 90
c = 129.684	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-09 
• Released Date: 2008-10-07 
Deposition Author(s): Bellon, S.F., D'Angelo, N., Whittington, D., Dussault, I.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations