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

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALK tyrosine kinase receptor327Homo sapiensMutation(s): 0 
Gene Names: ALK
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 6YL

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 51.74α = 90
b = 57.07β = 90
c = 104.58γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
xia2data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Data collection, Derived calculations
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description