3C1X | pdb_00003c1x

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

• PDB DOI: https://doi.org/10.2210/pdb3C1X/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2008-01-24 Released: 2008-03-18 
• Deposition Author(s): Sack, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.262 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

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

• PubMed: 18289854 
• DOI: https://doi.org/10.1016/j.bmcl.2008.01.121
• Primary Citation 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.

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Organizational Affiliation: 
• Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA. [e-mail]

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: 42.38 kDa 
• Atom Count: 2,440 
• Modeled Residue Count: 290 
• Deposited Residue Count: 373 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	373	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CKK	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
ID	Source	Binding 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), 0.238 (DCC) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.781	α = 90
b = 46.153	β = 90
c = 151.022	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
BUSTER-TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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