5KZ0

Structure of Human Anaplastic Lymphoma Kinase in Complex With 2-[(1R)-1-{[2-amino-5-(1,3-dimethyl-1H-pyrazol-4-yl)pyridin-3-yl]oxy}ethyl]-4-fluoro-N,N-dimethylbenzamide

• PDB DOI:  https://doi.org/10.2210/pdb5KZ0/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-07-22 Released: 2016-08-17 
• Deposition Author(s): McTigue, M., Deng, Y.L., Liu, W., Brooun, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.180 

Literature

Discovery of (10R)-7-amino-12-fluoro-2,10,16-trimethyl-15-oxo-10,15,16,17-tetrahydro-2H-8,4-(metheno)pyrazolo[4,3-h][2,5,11]-benzoxadiazacyclotetradecine-3-carbonitrile (PF-06463922), a macrocyclic inhibitor of anaplastic lymphoma kinase (ALK) and c-ros oncogene 1 (ROS1) with preclinical brain exposure and broad-spectrum potency against ALK-resistant mutations.

Johnson, T.W., Richardson, P.F., Bailey, S., Brooun, A., Burke, B.J., Collins, M.R., Cui, J.J., Deal, J.G., Deng, Y.L., Dinh, D., Engstrom, L.D., He, M., Hoffman, J., Hoffman, R.L., Huang, Q., Kania, R.S., Kath, J.C., Lam, H., Lam, J.L., Le, P.T., Lingardo, L., Liu, W., McTigue, M., Palmer, C.L., Sach, N.W., Smeal, T., Smith, G.L., Stewart, A.E., Timofeevski, S., Zhu, H., Zhu, J., Zou, H.Y., Edwards, M.P.

(2014) J Med Chem 57: 4720-4744

• PubMed: 24819116 
• DOI: https://doi.org/10.1021/jm500261q
• Primary Citation of Related Structures:  
  4CLI, 4CLJ, 4CMO, 4CMT, 4CMU, 4CNH, 4CTB, 4CTC, 5KZ0


• PubMed Abstract: 
  

Although crizotinib demonstrates robust efficacy in anaplastic lymphoma kinase (ALK)-positive non-small-cell lung carcinoma patients, progression during treatment eventually develops. Resistant patient samples revealed a variety of point mutations in the kinase domain of ALK, including the L1196M gatekeeper mutation. In addition, some patients progress due to cancer metastasis in the brain. Using structure-based drug design, lipophilic efficiency, and physical-property-based optimization, highly potent macrocyclic ALK inhibitors were prepared with good absorption, distribution, metabolism, and excretion (ADME), low propensity for p-glycoprotein 1-mediated efflux, and good passive permeability. These structurally unusual macrocyclic inhibitors were potent against wild-type ALK and clinically reported ALK kinase domain mutations. Significant synthetic challenges were overcome, utilizing novel transformations to enable the use of these macrocycles in drug discovery paradigms. This work led to the discovery of 8k (PF-06463922), combining broad-spectrum potency, central nervous system ADME, and a high degree of kinase selectivity.

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Organizational Affiliation: 

La Jolla Laboratories, Pfizer Worldwide Research and Development , 10770 Science Center Drive, San Diego, California 92121, United States.

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: 37.31 kDa 
• Atom Count: 2,527 
• Modelled Residue Count: 293 
• 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6YL	B [auth A]	2-[(1~{R})-1-[2-azanyl-5-(1,3-dimethylpyrazol-4-yl)pyridin-3-yl]oxyethyl]-4-fluoranyl-~{N},~{N}-dimethyl-benzamide C21 H24 F N5 O2 CZKOZZRYDBLSRF-CYBMUJFWSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6YL	BindingDB:  5KZ0	Ki: min: 22, max: 310 (nM) from 2 assay(s)
	Binding MOAD:  5KZ0	Ki: 22 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.74	α = 90
b = 57.07	β = 90
c = 104.58	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
SCALA	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): McTigue, M., Deng, Y.L., Liu, W., Brooun, A.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Data collection, Derived calculations