Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.36 kDa 
• Atom Count: 2631 
• Modelled Residue Count: 303 
• Deposited Residue Count: 367 
• Unique protein chains: 1

4MKC

Crystal Structure of Anaplastic Lymphoma Kinase Complexed with LDK378

• PDB DOI: 10.2210/pdb4MKC/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-09-04 Released: 2014-04-09 
• Deposition Author(s): Lee, C.C., Spraggon, G.

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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 

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

• PubMed: 24675041 
• 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-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	367	Homo sapiens	Mutation(s): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4MK	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 VERWOWGGCGHDQE-UHFFFAOYSA-N
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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

• 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 = 51.64	α = 90
b = 57.65	β = 90
c = 105.99	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-04 
• Released Date: 2014-04-09 
Deposition Author(s): Lee, C.C., Spraggon, G.

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