5FTO

Crystal structure of the ALK kinase domain in complex with Entrectinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Entrectinib: A New 3-Aminoindazole as a Potent Anaplastic Lymphoma Kinase (Alk), C-Ros Oncogene 1 Kinase (Ros1), and Pan-Tropomyosin Receptor Kinases (Pan-Trks) Inhibitor.

Menichincheri, M.Ardini, E.Magnaghi, P.Avanzi, N.Banfi, P.Bossi, R.T.Buffa, L.Canevari, G.Ceriani, L.Colombo, M.Corti, L.Donati, D.Fasolini, M.Felder, E.R.Fiorelli, C.Fiorentini, F.Galvani, A.Isacchi, A.Borgia, A.L.Marchionni, C.Nesi, M.Orrenius, C.Panzeri, A.Pesenti, E.Rusconi, L.Saccardo, B.M.Vanotti, E.Perrone, E.Orsini, P.

(2016) J Med Chem 59: 3392

  • DOI: 10.1021/acs.jmedchem.6b00064
  • Primary Citation of Related Structures:  
    5FTO, 5FTQ

  • PubMed Abstract: 
  • Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase responsible for the development of different tumor types. Despite the remarkable clinical activity of crizotinib (Xalkori), the first ALK inhibitor approved in 2011, the emergence of resistance mutations and of brain metastases frequently causes relapse in patients ...

    Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase responsible for the development of different tumor types. Despite the remarkable clinical activity of crizotinib (Xalkori), the first ALK inhibitor approved in 2011, the emergence of resistance mutations and of brain metastases frequently causes relapse in patients. Within our ALK drug discovery program, we identified compound 1, a novel 3-aminoindazole active on ALK in biochemical and in cellular assays. Its optimization led to compound 2 (entrectinib), a potent orally available ALK inhibitor active on ALK-dependent cell lines, efficiently penetrant the blood-brain barrier (BBB) in different animal species and highly efficacious in in vivo xenograft models. Moreover, entrectinib resulted to be strictly potent on the closely related tyrosine kinases ROS1 and TRKs recently found constitutively activated in several tumor types. Entrectinib is currently undergoing phase I/II clinical trial for the treatment of patients affected by ALK-, ROS1-, and TRK-positive tumors.


    Organizational Affiliation

    Oncology, Nerviano Medical Sciences Srl , Viale Pasteur 10, 20014 Nerviano, Milan, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALK TYROSINE KINASE RECEPTORA315Homo sapiensMutation(s): 0 
Gene Names: ALK
EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
NIH Common Fund Data Resources
PHAROS  Q9UM73
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YMX
Query on YMX

Download CCD File 
A
Entrectinib
C31 H34 F2 N6 O2
HAYYBYPASCDWEQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YMXIC50:  12   nM  BindingDB
YMXKi:  6.199999809265137   nM  BindingDB
YMXIC50:  55   nM  BindingDB
YMXIC50:  12   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.435α = 90
b = 58.471β = 90
c = 105.089γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references