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: 35.9 kDa 
• Atom Count: 2,567 
• Modelled Residue Count: 298 
• Deposited Residue Count: 315 
• Unique protein chains: 1

 5FTO

Crystal structure of the ALK kinase domain in complex with Entrectinib

• PDB DOI: 10.2210/pdb5FTO/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-01-14 Released: 2016-04-06 
• Deposition Author(s): Bossi, R., Canevari, G., Fasolini, M., Menichincheri, M., Ardini, E., Magnaghi, P., Avanzi, N., Banfi, P., Buffa, L., Ceriani, L., Colombo, M., Corti, L., Donati, D., Felder, E., Fiorelli, C., Fiorentini, F., Galvani, A., Isacchi, A., Lombardi Borgia, A., Marchionni, C., Nesi, M., Orrenius, C., Panzeri, A., Perrone, E., Pesenti, E., Rusconi, L., Saccardo, M.B., Vanotti, E., Orsini, P.

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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 

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

• PubMed: 27003761 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK TYROSINE KINASE RECEPTOR	A	315	Homo sapiens	Mutation(s): 0  Gene Names: ALK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens) Explore Q9UM73  Go to UniProtKB:  Q9UM73
PHAROS:  Q9UM73

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YMX	B [auth A]	Entrectinib C31 H34 F2 N6 O2 HAYYBYPASCDWEQ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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

• 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 = 52.435	α = 90
b = 58.471	β = 90
c = 105.089	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Bossi, R., Canevari, G., Fasolini, M., Menichincheri, M., Ardini, E., Magnaghi, P., Avanzi, N., Banfi, P., Buffa, L., Ceriani, L., Colombo, M., Corti, L., Donati, D., Felder, E., Fiorelli, C., Fiorentini, F., Galvani, A., Isacchi, A., Lombardi Borgia, A., Marchionni, C., Nesi, M., Orrenius, C., Panzeri, A., Perrone, E., Pesenti, E., Rusconi, L., Saccardo, M.B., Vanotti, E., Orsini, P.

Revision History  

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