Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 37.39 kDa 
• Atom Count: 2330 
• Residue Count: 287 
• Unique protein chains: 1

4FNZ

Crystal structure of human anaplastic lymphoma kinase in complex with piperidine-carboxamide inhibitor 2

• DOI: 10.2210/pdb4FNZ/pdb

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


• Deposited: 2012-06-20 Released: 2012-08-29 
• Deposition Author(s): Whittington, D.A., Epstein, L.F., Chen, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• R-Value Observed: 0.202 

Literature

The R1275Q Neuroblastoma Mutant and Certain ATP-competitive Inhibitors Stabilize Alternative Activation Loop Conformations of Anaplastic Lymphoma Kinase.

Epstein, L.F., Chen, H., Emkey, R., Whittington, D.A.

(2012) J Biol Chem 287: 37447-37457

• PubMed: 22932897 
• DOI: 10.1074/jbc.M112.391425
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that, when genetically altered by mutation, amplification, chromosomal translocation or inversion, has been shown to play an oncogenic role in certain cancers. Small molecule inhibitors targeting the kinase activity of ALK have proven to be effective therapies in certain ALK-driven malignancies and one such inhibitor, crizotinib, is now approved for the treatment of EML4-ALK-driven, non-small cell lung cancer. In neuroblastoma, activating point mutations in the ALK kinase domain can drive disease progression, with the two most common mutations being F1174L and R1275Q. We report here crystal structures of the ALK kinase domain containing the F1174L and R1275Q mutations. Also included are crystal structures of ALK in complex with novel small molecule ALK inhibitors, including a classic type II inhibitor, that stabilize previously unobserved conformations of the ALK activation loop. Collectively, these structures illustrate a different series of activation loop conformations than has been observed in previous ALK crystal structures and provide insight into the activating nature of the R1275Q mutation. The novel active site topologies presented here may also aid the structure-based drug design of a new generation of ALK inhibitors.

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Organizational Affiliation: 

Department of Molecular Structure and Characterization, Amgen Inc., Cambridge, Massachusetts 02142, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALK tyrosine kinase receptor	A	327	Homo sapiens	Mutation(s): 1  Gene Names: ALK EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens) Go to UniProtKB:  Q9UM73
NIH Common Fund Data Resources
PHAROS  Q9UM73 GTEx  ENSG00000171094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NZF	A	(3S)-N-[3-(trifluoromethoxy)benzyl]-1-{2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}piperidine-3-carboxamide C27 H30 F3 N5 O5 LDRVTAIULYJYRP-SFHVURJKSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
NZF	IC50:  16   nM  BindingDB
NZF	IC50 :  16   nM  PDBBind
NZF	IC50:  59   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.496	α = 90
b = 58.059	β = 90
c = 105.046	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-20 
• Released Date: 2012-08-29 
Deposition Author(s): Whittington, D.A., Epstein, L.F., Chen, H.

Revision History 

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description