8ARJ | pdb_00008arj

Anaplastic Lymphoma Kinase with a novel carboline inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8ARJ/pdb

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


• Deposited: 2022-08-17 Released: 2022-09-14 
• Deposition Author(s): Mologni, L., Scapozza, L., Gambacorti-Passerini, C., Tardy, S., Goekjian, P., Robinson, C., Brown, D.
• Funding Organization(s): Other government, Italian Association for Cancer Research, European Commission

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.229 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Discovery of Novel alpha-Carboline Inhibitors of the Anaplastic Lymphoma Kinase.

Mologni, L., Tardy, S., Zambon, A., Orsato, A., Bisson, W.H., Ceccon, M., Viltadi, M., D'Attoma, J., Pannilunghi, S., Vece, V., Bertho, J., Goekjian, P., Scapozza, L., Gambacorti-Passerini, C.

(2022) ACS Omega 7: 17083-17097

• PubMed: 35647450 
• DOI: https://doi.org/10.1021/acsomega.2c00507
• Primary Citation Related Structures: 
  8ARJ


• PubMed Abstract: 
  

  The anaplastic lymphoma kinase (ALK) is abnormally expressed and hyperactivated in a number of tumors and represents an ideal therapeutic target. Despite excellent clinical responses to ALK inhibition, drug resistance still represents an issue and novel compounds that overcome drug-resistant mutants are needed. We designed, synthesized, and evaluated a large series of azacarbazole inhibitors. Several lead compounds endowed with submicromolar potency were identified. Compound 149 showed selective inhibition of native and mutant drug-refractory ALK kinase in vitro as well as in a Ba/F3 model and in human ALK+ lymphoma cells. The three-dimensional (3D) structure of a 149 :ALK-KD cocrystal is reported, showing extensive interaction through the hinge region and the catalytic lysine 1150.

---

Organizational Affiliation: 
• Dept. of Medicine and Surgery, University of Milano-Bicocca, Monza 20900, Italy.
Galkem srl, Monza 20900, Italy.
Laboratoire Chimie Organique 2-Glycochimie, CNRS-Université Claude Bernard Lyon 1, Lyon 69100, France.
School of Pharmaceutical Sciences, University of Geneva, Geneva 1211, Switzerland.
Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva 1211, Switzerland.
Department of Chemistry and Geological Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
Department of Chemistry, Universidade Estadual de Londrina, Paraná 86057-970, Brazil.
Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97227, United States.
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.46 kDa 
• Atom Count: 2,221 
• Modeled Residue Count: 275 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	321	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 GTEx:  ENSG00000171094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NRR (Subject of Investigation/LOI)	B [auth A]	3-(dimethylamino)-1-[3-[4-(4-methylpiperazin-1-yl)phenyl]-9~{H}-pyrido[2,3-b]indol-6-yl]prop-2-en-1-one C27 H29 N5 O JFOIWAWELQEHHK-KHPPLWFESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.229 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.714	α = 90
b = 56.593	β = 90
c = 103.243	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Mologni, L., Scapozza, L., Gambacorti-Passerini, C., Tardy, S., Goekjian, P., Robinson, C., Brown, D.

---

Funding Organization	Location	Grant Number
Other government	Italy	Italian Ministry of Research 3/13
Italian Association for Cancer Research	Italy	IG-24828
European Commission	European Union	ITN 675712 and 503467

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description