4MKC

Crystal Structure of Anaplastic Lymphoma Kinase Complexed with LDK378

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

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: 10.1158/2159-8290.CD-13-0846
  • Primary Citation of Related Structures:  
    4MKC

  • 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-gen ...

    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: 

    Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALK tyrosine kinase receptorA367Homo sapiensMutation(s): 1 
Gene Names: ALK
EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
NIH Common Fund Data Resources
PHAROS  Q9UM73
GTEx  ENSG00000171094
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4MK
Query on 4MK
Download Ideal Coordinates CCD File 
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
VERWOWGGCGHDQE-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4MKIC50:  14   nM  BindingDB
4MKIC50:  5   nM  BindingDB
4MKIC50:  2.200000047683716   nM  BindingDB
4MKIC50:  4.599999904632568   nM  BindingDB
4MKIC50:  1   nM  BindingDB
4MKIC50:  29   nM  BindingDB
4MKIC50:  3.4000000953674316   nM  BindingDB
4MKIC50:  91   nM  BindingDB
4MKIC50:  2.299999952316284   nM  BindingDB
4MKIC50:  2.9000000953674316   nM  BindingDB
4MKIC50:  5   nM  BindingDB
4MKIC50:  26   nM  BindingDB
4MKIC50:  2.5   nM  BindingDB
4MKIC50:  41   nM  BindingDB
4MKKd:  1.2999999523162842   nM  BindingDB
4MKIC50:  0.20000000298023224   nM  BindingDB
4MKIC50:  35   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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