4FOB

Crystal structure of human anaplastic lymphoma kinase in complex with acyliminobenzimidazole inhibitor 1

• PDB DOI: https://doi.org/10.2210/pdb4FOB/pdb

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


• Deposited: 2012-06-20 Released: 2012-07-11 
• Deposition Author(s): Whittington, D.A., Epstein, L.F., Chen, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

The Discovery and Optimization of a Novel Class of Potent, Selective, and Orally Bioavailable Anaplastic Lymphoma Kinase (ALK) Inhibitors with Potential Utility for the Treatment of Cancer.

Lewis, R.T., Bode, C.M., Choquette, D.M., Potashman, M., Romero, K., Stellwagen, J.C., Teffera, Y., Moore, E., Whittington, D.A., Chen, H., Epstein, L.F., Emkey, R., Andrews, P.S., Yu, V.L., Saffran, D.C., Xu, M., Drew, A., Merkel, P., Szilvassy, S., Brake, R.L.

(2012) J Med Chem 55: 6523-6540

• PubMed: 22734674 
• DOI: https://doi.org/10.1021/jm3005866
• Primary Citation of Related Structures:  
  4FOB, 4FOC, 4FOD


• PubMed Abstract: 
  

  A class of 2-acyliminobenzimidazoles has been developed as potent and selective inhibitors of anaplastic lymphoma kinase (ALK). Structure based design facilitated the rapid development of structure-activity relationships (SAR) and the optimization of kinase selectivity. Introduction of an optimally placed polar substituent was key to solving issues of metabolic stability and led to the development of potent, selective, orally bioavailable ALK inhibitors. Compound 49 achieved substantial tumor regression in an NPM-ALK driven murine tumor xenograft model when dosed qd. Compounds 36 and 49 show favorable potency and PK characteristics in preclinical species indicative of suitability for further development.

---

Organizational Affiliation: 

Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 40.62 kDa 
• Atom Count: 2,556 
• Modelled Residue Count: 295 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	353	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 GTEx:  ENSG00000171094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0US	B [auth A]	N-{1-[cis-4-(hydroxymethyl)cyclohexyl]-5-(piperidin-1-ylmethyl)-1H-benzimidazol-2-yl}-3-(prop-2-en-1-ylsulfamoyl)benzamide C30 H39 N5 O4 S LWJAHJMKAARBCO-WZJNIGMMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0US	PDBBind:  4FOB	IC50: 5 (nM) from 1 assay(s)
	BindingDB:  4FOB	IC50: min: 5, max: 48 (nM) from 2 assay(s)
	Binding MOAD:  4FOB	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.624	α = 90
b = 57.525	β = 90
c = 105.521	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Whittington, D.A., Epstein, L.F., Chen, H.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations