Structure of L1196M Mutant Anaplastic Lymphoma Kinase in Complex with Crizotinib

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Design of Potent and Selective Inhibitors to Overcome Clinical Anaplastic Lymphoma Kinase Mutations Resistant to Crizotinib.

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

(2014) J Med Chem 57: 1170

  • DOI: https://doi.org/10.1021/jm401805h
  • Primary Citation of Related Structures:  
    2YFX, 2YHV, 4ANL, 4ANQ, 4CCB, 4CCU, 4CD0

  • PubMed Abstract: 

    Crizotinib (1), an anaplastic lymphoma kinase (ALK) receptor tyrosine kinase inhibitor approved by the U.S. Food and Drug Administration in 2011, is efficacious in ALK and ROS positive patients. Under pressure of crizotinib treatment, point mutations arise in the kinase domain of ALK, resulting in resistance and progressive disease. The successful application of both structure-based and lipophilic-efficiency-focused drug design resulted in aminopyridine 8e, which was potent across a broad panel of engineered ALK mutant cell lines and showed suitable preclinical pharmacokinetics and robust tumor growth inhibition in a crizotinib-resistant cell line (H3122-L1196M).

  • 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
TYROSINE-PROTEIN KINASE RECEPTOR327Homo sapiensMutation(s): 1 
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 VGH

Download Ideal Coordinates CCD File 
B [auth A]3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine
C21 H22 Cl2 F N5 O
Binding Affinity Annotations 
IDSourceBinding Affinity
VGH BindingDB:  2YFX Ki: min: 0.74, max: 8.2 (nM) from 2 assay(s)
Kd: min: 3.3, max: 4.4 (nM) from 3 assay(s)
IC50: min: 0.64, max: 3039 (nM) from 66 assay(s)
EC50: min: 575, max: 2.28e+4 (nM) from 3 assay(s)
PDBBind:  2YFX Ki: 8.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.721α = 90
b = 57.174β = 90
c = 105.253γ = 90
Software Package:
Software NamePurpose
XDSdata 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: 2011-05-04
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references, Derived calculations, Other, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description