5EYD | pdb_00005eyd

Crystal structure of c-Met in complex with AMG 337

• PDB DOI: https://doi.org/10.2210/pdb5EYD/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2015-11-24 Released: 2016-02-10 
• Deposition Author(s): Whittington, D.A., Long, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.249 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Discovery of (R)-6-(1-(8-Fluoro-6-(1-methyl-1H-pyrazol-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3-yl)ethyl)-3-(2-methoxyethoxy)-1,6-naphthyridin-5(6H)-one (AMG 337), a Potent and Selective Inhibitor of MET with High Unbound Target Coverage and Robust In Vivo Antitumor Activity.

Boezio, A.A., Copeland, K.W., Rex, K., K Albrecht, B., Bauer, D., Bellon, S.F., Boezio, C., Broome, M.A., Choquette, D., Coxon, A., Dussault, I., Hirai, S., Lewis, R., Lin, M.H., Lohman, J., Liu, J., Peterson, E.A., Potashman, M., Shimanovich, R., Teffera, Y., Whittington, D.A., Vaida, K.R., Harmange, J.C.

(2016) J Med Chem 59: 2328-2342

• PubMed: 26812066 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01716
• Primary Citation Related Structures: 
  5EYC, 5EYD


• PubMed Abstract: 
  

  Deregulation of the receptor tyrosine kinase mesenchymal epithelial transition factor (MET) has been implicated in several human cancers and is an attractive target for small molecule drug discovery. Herein, we report the discovery of compound 23 (AMG 337), which demonstrates nanomolar inhibition of MET kinase activity, desirable preclinical pharmacokinetics, significant inhibition of MET phosphorylation in mice, and robust tumor growth inhibition in a MET-dependent mouse efficacy model.

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Organizational Affiliation: 
• Amgen Incorporated , 360 Binney Street, Cambridge, Massachusetts 02142, United States.
Amgen Incorporated , One Amgen Center Drive, Thousand Oaks, California 91320, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.68 kDa 
• Atom Count: 2,598 
• Modeled Residue Count: 289 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	309	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000105976

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5T1	B [auth A]	6-[(1~{R})-1-[8-fluoranyl-6-(1-methylpyrazol-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3-yl]ethyl]-3-(2-methoxyethoxy)-1,6-naphthyridin-5-one C23 H22 F N7 O3 DWHXUGDWKAIASB-CQSZACIVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.249 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.848	α = 90
b = 43.344	β = 90
c = 158.345	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Whittington, D.A., Long, A.M.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2016-04-06
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description