Crystal structure of the ALK kinase domain in complex with Entrectinib

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/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. 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

    Accelera Srl , Viale Pasteur 10, 20014 Nerviano, Milan, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALK TYROSINE KINASE RECEPTOR315Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
GTEx:  ENSG00000171094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM73
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on YMX

Download Ideal Coordinates CCD File 
B [auth A]Entrectinib
C31 H34 F2 N6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
YMX Binding MOAD:  5FTO Ki: 6.2 (nM) from 1 assay(s)
BindingDB:  5FTO Ki: 6.2 (nM) from 1 assay(s)
IC50: min: 12, max: 55 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description