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.

Macromolecule Content

• Total Structure Weight: 37.40 kDa 
• Atom Count: 2465 
• Modelled Residue Count: 285 
• Deposited Residue Count: 327 
• Unique protein chains: 1

5IUG

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

• PDB DOI: 10.2210/pdb5IUG/pdb

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


• 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 
• R-Value Observed: 0.184 

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:  
  5IUG, 5IUH, 5IUI


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	327	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
729	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
729	BindingDB:  5IUG	Kd: 2.4 (nM) from 1 assay(s)
		IC50: 177 (nM) from 1 assay(s)
	Binding MOAD:  5IUG	IC50: 177 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.913	α = 90
b = 56.495	β = 90
c = 102.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
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
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Database references, Derived calculations