4R1Y | pdb_00004r1y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.238 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4R1Y

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2015.02.002
  • Primary Citation 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. 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. Electronic address: dieter.dorsch@merckgroup.com.

Macromolecule Content 

  • Total Structure Weight: 34.18 kDa 
  • Atom Count: 2,333 
  • Modeled Residue Count: 265 
  • Deposited Residue Count: 292 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor292Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3EH

Query on 3EH



Download:Ideal Coordinates CCD File
B [auth A]3-(diethylamino)propyl (3-{[5-(3,4-dimethoxyphenyl)-2-oxo-2H-1,3,4-thiadiazin-3(6H)-yl]methyl}phenyl)carbamate
C26 H34 N4 O5 S
WVYHFPSGWCCXMO-UHFFFAOYSA-N
7PE

Query on 7PE



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3EH BindingDB:  4R1Y IC50: min: 400, max: 1100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.238 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.157α = 90
b = 42.882β = 90
c = 169.502γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations