4FNZ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


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

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

  • DOI: 10.1074/jbc.M112.391425
  • Primary Citation of Related Structures:  

  • 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 t ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALK tyrosine kinase receptor
A
327Homo sapiensMutation(s): 1 
Gene Names: ALK
EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens)
Go to Gene View: ALK
Go to UniProtKB:  Q9UM73
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NZF
Query on NZF
Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NZFIC50: 16 - 59 nM (99) BINDINGDB
NZFIC50: 16 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.496α = 90.00
b = 58.059β = 90.00
c = 105.046γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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