3ZCL | pdb_00003zcl

X-ray Structure of c-Met kinase in complex with inhibitor (S)-3-(1-(1H-pyrrolo(2,3-b)pyridin-3-yl)ethyl)-N-isopropyl-(1,2,4)triazolo(4,3- b)pyridazin-6-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.211 (Depositor) 
  • R-Value Work: 
    0.193 (Depositor) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3ZCL

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Lessons from (S)-6-(1-(6-(1-Methyl-1H-Pyrazol-4-Yl)-[1,2, 4]Triazolo[4,3-B]Pyridazin-3-Yl)Ethyl)Quinoline (Pf-04254644), an Inhibitor of Receptor Tyrosine Kinase C-met with High Protein Kinase Selectivity But Broad Phosphodiesterase Family Inhibition Leading to Myocardial Degeneration in Rats.

Cui, J.J.Shen, H.Tran-Dube, M.Nambu, M.Mctigue, M.Grodsky, N.Ryan, K.Yamazaki, S.Aguirre, S.Parker, M.Li, Q.Zou, H.Christensen, J.

(2013) J Med Chem 56: 6651

  • DOI: https://doi.org/10.1021/jm400926x
  • Primary Citation Related Structures: 
    3ZBX, 3ZC5, 3ZCL

  • PubMed Abstract: 

    The hepatocyte growth factor (HGF)/c-Met signaling axis is deregulated in many cancers and plays important roles in tumor invasive growth and metastasis. An exclusively selective c-Met inhibitor (S)-6-(1-(6-(1-methyl-1H-pyrazol-4-yl)-[1,2,4]triazolo[4,3-b]pyridazin-3-yl)ethyl)quinoline (8) was discovered from a highly selective high-throughput screening hit via structure-based drug design and medicinal chemistry lead optimization. Compound 8 had many attractive properties meriting preclinical evaluation. Broad off-target screens identified 8 as a pan-phosphodiesterase (PDE) family inhibitor, which was implicated in a sustained increase in heart rate, increased cardiac output, and decreased contractility indices, as well as myocardial degeneration in in vivo safety evaluations in rats. Compound 8 was terminated as a preclinical candidate because of a narrow therapeutic window in cardio-related safety. The learning from multiparameter lead optimization and strategies to avoid the toxicity attrition at the late stage of drug discovery are discussed.


  • Organizational Affiliation
    • La Jolla Laboratories, Pfizer Worldwide Research and Development , 10770 Science Center Drive, San Diego, California 92121, United States.

Macromolecule Content 

  • Total Structure Weight: 35.2 kDa 
  • Atom Count: 2,670 
  • Modeled Residue Count: 291 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HEPATOCYTE GROWTH FACTOR RECEPTOR306Homo sapiensMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5TF

Query on 5TF



Download:Ideal Coordinates CCD File
B [auth A](S)-3-(1-(1H-pyrrolo(2,3-b)pyridin-3-yl)ethyl)-N-isopropyl-(1,2,4)triazolo(4,3-b)pyridazin-6-amine
C17 H19 N7
PUIUZHJXBDSQEZ-NSHDSACASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5TF BindingDB:  3ZCL Ki: 10 (nM) from 1 assay(s)
IC50: 19 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.211 (Depositor) 
  • R-Value Work:  0.193 (Depositor) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.997α = 90
b = 94.509β = 90
c = 46.834γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description