7R7K | pdb_00007r7k

Structure of Human Anaplastic Lymphoma Kinase Domain in complex with (4-[6-amino-5-[(1~{R})-1-[5-fluoro-2-(triazol-2-yl)phenyl]ethoxy]-3-pyridyl]isoindolin-1-one)

• PDB DOI: https://doi.org/10.2210/pdb7R7K/pdb

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


• Deposited: 2021-06-24 Released: 2022-06-29 
• Deposition Author(s): McTigue, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.221 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Analysis of lorlatinib analogs reveals a roadmap for targeting diverse compound resistance mutations in ALK-positive lung cancer.

Shiba-Ishii, A., Johnson, T.W., Dagogo-Jack, I., Mino-Kenudson, M., Johnson, T.R., Wei, P., Weinrich, S.L., McTigue, M.A., Walcott, M.A., Nguyen-Phuong, L., Dionne, K., Acker, A., Kiedrowski, L.A., Do, A., Peterson, J.L., Barth, J.L., Yeap, B.Y., Gainor, J.F., Lin, J.J., Yoda, S., Hata, A.N.

(2022) Nat Cancer 3: 710-722

• PubMed: 35726063 
• DOI: https://doi.org/10.1038/s43018-022-00399-6
• Primary Citation Related Structures: 
  7R7K, 7R7R


• PubMed Abstract: 
  

  Lorlatinib is currently the most advanced, potent and selective anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitor for the treatment of ALK-positive non-small cell lung cancer in the clinic; however, diverse compound ALK mutations driving therapy resistance emerge. Here, we determine the spectrum of lorlatinib-resistant compound ALK mutations in patients, following treatment with lorlatinib, the majority of which involve ALK G1202R or I1171N/S/T. We further identify structurally diverse lorlatinib analogs that harbor differential selective profiles against G1202R versus I1171N/S/T compound ALK mutations. Structural analysis revealed increased potency against compound mutations through improved inhibition of either G1202R or I1171N/S/T mutant kinases. Overall, we propose a classification of heterogenous ALK compound mutations enabling the development of distinct therapeutic strategies for precision targeting following sequential tyrosine kinase inhibitors.

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Organizational Affiliation: 
• Massachusetts General Hospital Cancer Center, Charlestown, MA, USA.
Pfizer Worldwide Research and Development, La Jolla, CA, USA.
Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Department of Pathology, Harvard Medical School, Boston, MA, USA.
Guardant Health, Redwood City, CA, USA.
Massachusetts General Hospital Cancer Center, Charlestown, MA, USA. [e-mail].
Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. [e-mail].
Massachusetts General Hospital Cancer Center, Charlestown, MA, USA. [e-mail].
Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. [e-mail].
Massachusetts General Hospital Cancer Center, Charlestown, MA, USA. [e-mail].
Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.34 kDa 
• Atom Count: 2,563 
• Modeled Residue Count: 290 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	327	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
25J (Subject of Investigation/LOI)	B [auth A]	4-(6-amino-5-{(1R)-1-[5-fluoro-2-(2H-1,2,3-triazol-2-yl)phenyl]ethoxy}pyridin-3-yl)-2,3-dihydro-1H-isoindol-1-one C23 H19 F N6 O2 CKJMFMVVGMXESQ-CYBMUJFWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.221 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.602	α = 90
b = 57.389	β = 90
c = 105.432	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): McTigue, M.

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2022-08-10
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description