Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37403.89 
• Atom Count: 2273 
• Residue Count: 327 
• Unique protein chains: 1

5IUG

Crystal Structure of Anaplastic Lymphoma Kinase (ALK) in complex with 5a

• DOI: 10.2210/pdb5IUG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 1 


• Deposited: 2016-03-18 Released: 2016-05-18 
• Deposition Author(s): Tu, C.H., Wu, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 

Literature

Pyrazolylamine Derivatives Reveal the Conformational Switching between Type I and Type II Binding Modes of Anaplastic Lymphoma Kinase (ALK).

Tu, C.H., Lin, W.H., Peng, Y.H., Hsu, T., Wu, J.S., Chang, C.Y., Lu, C.T., Lyu, P.C., Shih, C., Jiaang, W.T., Wu, S.Y.

(2016) J.Med.Chem. 59: 3906-3919

• PubMed: 27031565 
• DOI: 10.1021/acs.jmedchem.6b00106
• Primary Citation of Related Structures:  
  5IUI, 5IUH


• PubMed Abstract: 
  

Most anaplastic lymphoma kinase (ALK) inhibitors adopt a type I binding mode, but only limited type II ALK structural studies are available. Herein, we present the structure of ALK in complex with N1-(3-4-[([5-(tert-butyl)-3-isoxazolyl]aminocarbonyl)amino]-3-methylphenyl-1H-5-pyrazolyl)-4-[(4-methylpiperazino)methyl]benzamide (5a), a novel ALK inhibitor adopting a type II binding mode. It revealed binding of 5a resulted in the conformational change and reposition of the activation loop, αC-helix, and juxtamembrane domain, which are all important domains for the autoinhibition mechanism and downstream signal pathway regulation of ALK. A structure-activity relationship study revealed that modifications to the structure of 5a led to significant differences in the ALK potency and altered the protein structure of ALK. To the best of our knowledge, this is the first structural biology study to directly observe how changes in the structure of a small molecule can regulate the switch between the type I and type II binding modes and induce dramatic conformational changes.

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Organizational Affiliation: 

Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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 Gene View: ALK Go to UniProtKB:  Q9UM73

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
729	A	N-[3-(4-{[(5-tert-butyl-1,2-oxazol-3-yl)carbamoyl]amino}-3-methylphenyl)-1H-pyrazol-5-yl]-4-[(4-methylpiperazin-1-yl)methyl]benzamide C31 H38 N8 O3 AEOFEGDYORZHFE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 51.913	α = 90.00
b = 56.495	β = 90.00
c = 102.710	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-18 
• Released Date: 2016-05-18 
• Deposition Author(s): Tu, C.H., Wu, S.Y.

Revision History 

• Version 1.0: 2016-05-18
  Type: Initial release