3C1X

Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-MET in complex with a Pyrrolotriazine based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CKKClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Identification of pyrrolo[2,1-f][1,2,4]triazine-based inhibitors of Met kinase.

Schroeder, G.M.Chen, X.T.Williams, D.K.Nirschl, D.S.Cai, Z.W.Wei, D.Tokarski, J.S.An, Y.Sack, J.Chen, Z.Huynh, T.Vaccaro, W.Poss, M.Wautlet, B.Gullo-Brown, J.Kellar, K.Manne, V.Hunt, J.T.Wong, T.W.Lombardo, L.J.Fargnoli, J.Borzilleri, R.M.

(2008) Bioorg Med Chem Lett 18: 1945-1951

  • DOI: https://doi.org/10.1016/j.bmcl.2008.01.121
  • Primary Citation of Related Structures:  
    3C1X

  • PubMed Abstract: 

    An amide library derived from the pyrrolo[2,1-f][1,2,4]triazine scaffold led to the identification of modest inhibitors of Met kinase activity. Introduction of polar side chains at C-6 of the pyrrolotriazine core provided significant improvements in in vitro potency. The amide moiety could be replaced with acylurea and malonamide substituents to give compounds with improved potency in the Met-driven GTL-16 human gastric carcinoma cell line. Acylurea pyrrolotriazines with substitution at C-5 demonstrated single digit nanomolar kinase activity. X-ray crystallography revealed that the C-5 substituted pyrrolotriazines bind to the Met kinase domain in an ATP-competitive manner.


  • Organizational Affiliation

    Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA. gretchen.schroeder@bms.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor373Homo sapiensMutation(s): 4 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CKK
Query on CKK

Download Ideal Coordinates CCD File 
B [auth A]N-{[4-({5-[(4-aminopiperidin-1-yl)methyl]pyrrolo[2,1-f][1,2,4]triazin-4-yl}oxy)-3-fluorophenyl]carbamoyl}-2-(4-fluorophenyl)acetamide
C27 H27 F2 N7 O3
YQQFRBUHZZNTGY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CKK BindingDB:  3C1X IC50: 45 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.781α = 90
b = 46.153β = 90
c = 151.022γ = 90
Software Package:
Software NamePurpose
AMoREphasing
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CKKClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2008-03-18 
  • Deposition Author(s): Sack, J.

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection