3U6H

Crystal structure of c-Met in complex with pyrazolone inhibitor 26

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.221 

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


Literature

Structure-based design of novel class II c-Met inhibitors: 1. Identification of pyrazolone-based derivatives.

Norman, M.H., Liu, L., Lee, M., Xi, N., Fellows, I., D'Angelo, N.D., Dominguez, C., Rex, K., Bellon, S.F., Kim, T.S., Dussault, I.

(2012) J Med Chem 55: 1858-1867

  • DOI: 10.1021/jm201330u
  • Primary Citation of Related Structures:  
    3U6H, 3U6I, 3U6J

  • PubMed Abstract: 

    • Deregulation of c-Met receptor tyrosine kinase activity leads to tumorigenesis and metastasis in animal models. More importantly, the identification of activating mutations in c-Met, as well as MET gene amplification in human cancers, points to c-Met as an important target for cancer therapy ...

    Deregulation of c-Met receptor tyrosine kinase activity leads to tumorigenesis and metastasis in animal models. More importantly, the identification of activating mutations in c-Met, as well as MET gene amplification in human cancers, points to c-Met as an important target for cancer therapy. We have previously described two classes of c-Met kinase inhibitors (class I and class II) that differ in their binding modes and selectivity profiles. The class II inhibitors tend to have activities on multiple kinases. Knowledge of the binding mode of these molecules in the c-Met protein led to the design and evaluation of several new class II c-Met inhibitors that utilize various 5-membered cyclic carboxamides to conformationally restrain key pharmacophoric groups within the molecule. These investigations resulted in the identification of a potent and novel class of pyrazolone c-Met inhibitors with good in vivo activity.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorA309Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
03X
Query on 03X
Download Ideal Coordinates CCD File 
B [auth A]N-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazole-4-carboxamide
C29 H25 F N4 O5
SBLMCLDRWJNEJK-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
03X PDBBind:  3U6H Ki: 1 (nM) from 1 assay(s)
Binding MOAD:  3U6H Ki: 1 (nM) from 1 assay(s)
BindingDB:  3U6H Ki: 1 (nM) from 1 assay(s)
IC50: min: 1, max: 20 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.61α = 90
b = 81.97β = 90
c = 127.038γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references