4FOB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/jm3005866
  • Primary Citation of Related Structures:  

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALK tyrosine kinase receptor
A
353Homo 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
0US
Query on 0US

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0USIC50: 5 - 48 nM (99) BINDINGDB
0USIC50: 5 nM BINDINGMOAD
0USIC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.624α = 90.00
b = 57.525β = 90.00
c = 105.521γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-15
    Type: Database references