Crystal Structure of Anaplastic Lymphoma Kinase Complexed with LDK378

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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This is version 1.3 of the entry. See complete history


The ALK Inhibitor Ceritinib Overcomes Crizotinib Resistance in Non-Small Cell Lung Cancer.

Friboulet, L.Li, N.Katayama, R.Lee, C.C.Gainor, J.F.Crystal, A.S.Michellys, P.Y.Awad, M.M.Yanagitani, N.Kim, S.Pferdekamper, A.C.Li, J.Kasibhatla, S.Sun, F.Sun, X.Hua, S.McNamara, P.Mahmood, S.Lockerman, E.L.Fujita, N.Nishio, M.Harris, J.L.Shaw, A.T.Engelman, J.A.

(2014) Cancer Discov 4: 662-673

  • DOI: https://doi.org/10.1158/2159-8290.CD-13-0846
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Non-small cell lung cancers (NSCLC) harboring anaplastic lymphoma kinase (ALK) gene rearrangements invariably develop resistance to the ALK tyrosine kinase inhibitor (TKI) crizotinib. Herein, we report the first preclinical evaluation of the next-generation ALK TKI, ceritinib (LDK378), in the setting of crizotinib resistance. An interrogation of in vitro and in vivo models of acquired resistance to crizotinib, including cell lines established from biopsies of patients with crizotinib-resistant NSCLC, revealed that ceritinib potently overcomes crizotinib-resistant mutations. In particular, ceritinib effectively inhibits ALK harboring L1196M, G1269A, I1171T, and S1206Y mutations, and a cocrystal structure of ceritinib bound to ALK provides structural bases for this increased potency. However, we observed that ceritinib did not overcome two crizotinib-resistant ALK mutations, G1202R and F1174C, and one of these mutations was identified in 5 of 11 biopsies from patients with acquired resistance to ceritinib. Altogether, our results demonstrate that ceritinib can overcome crizotinib resistance, consistent with clinical data showing marked efficacy of ceritinib in patients with crizotinib-resistant disease.

  • Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALK tyrosine kinase receptor367Homo sapiensMutation(s): 1 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4MK

Download Ideal Coordinates CCD File 
D [auth A]5-chloro-N~2~-[5-methyl-4-(piperidin-4-yl)-2-(propan-2-yloxy)phenyl]-N~4~-[2-(propan-2-ylsulfonyl)phenyl]pyrimidine-2,4-diamine
C28 H36 Cl N5 O3 S
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
4MK BindingDB:  4MKC Ki: 3700 (nM) from 1 assay(s)
Kd: 1.3 (nM) from 1 assay(s)
IC50: min: 0.2, max: 810 (nM) from 46 assay(s)
EC50: min: 3210, max: 3490 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.64α = 90
b = 57.65β = 90
c = 105.99γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary