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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


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

  • 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. richard.lewis@amgen.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALK tyrosine kinase receptor353Homo sapiensMutation(s): 1 
Gene Names: ALK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
GTEx:  ENSG00000171094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM73
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0US

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 51.624α = 90
b = 57.525β = 90
c = 105.521γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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