4R1V

Identification and optimization of pyridazinones as potent and selective c-Met kinase inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


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


Literature

Identification and optimization of pyridazinones as potent and selective c-Met kinase inhibitors.

Dorsch, D., Schadt, O., Stieber, F., Meyring, M., Gradler, U., Bladt, F., Friese-Hamim, M., Knuhl, C., Pehl, U., Blaukat, A.

(2015) Bioorg Med Chem Lett 25: 1597-1602

  • DOI: 10.1016/j.bmcl.2015.02.002
  • Primary Citation of Related Structures:  
    4R1V, 4R1Y

  • PubMed Abstract: 

    • In a high-throughput screening campaign for c-Met kinase inhibitors, a thiadiazinone derivative with a carbamate group was identified as a potent in vitro inhibitor. Subsequent optimization guided by c-Met-inhibitor X-ray structures furnished new compound classes with excellent in vitro and in vivo profiles ...

    In a high-throughput screening campaign for c-Met kinase inhibitors, a thiadiazinone derivative with a carbamate group was identified as a potent in vitro inhibitor. Subsequent optimization guided by c-Met-inhibitor X-ray structures furnished new compound classes with excellent in vitro and in vivo profiles. The thiadiazinone ring of the HTS hit was first replaced by a pyridazinone followed by an exchange of the carbamate hinge binder with a 1,5-disubstituted pyrimidine. Finally an optimized compound, 22 (MSC2156119), with excellent in vitro potency, high kinase selectivity, long half-life after oral administration and in vivo anti-tumor efficacy at low doses, was selected as a candidate for clinical development.

    Organizational Affiliation: 

    Merck Serono Research & Development, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor A291Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3E8
Query on 3E8
Download Ideal Coordinates CCD File 
A
3-[1-(3-{5-[(1-methylpiperidin-4-yl)methoxy]pyrimidin-2-yl}benzyl)-6-oxo-1,6-dihydropyridazin-3-yl]benzonitrile
C29 H28 N6 O2
AHYMHWXQRWRBKT-UHFFFAOYSA-N		 Ligand Interaction
GBL
Query on GBL
Download Ideal Coordinates CCD File 
A
GAMMA-BUTYROLACTONE
C4 H6 O2
YEJRWHAVMIAJKC-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3E8IC50:  3   nM  BindingDB
3E8IC50:  12   nM  BindingDB
3E8IC50:  100   nM  BindingDB
3E8IC50:  400   nM  Binding MOAD
3E8IC50:  1   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38α = 90
b = 43.038β = 92.23
c = 84.844γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references