4FOC

Crystal structure of human anaplastic lymphoma kinase in complex with acyliminobenzimidazole inhibitor 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALK tyrosine kinase receptorA353Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0UU (Subject of Investigation/LOI)
Query on 0UU

Download Ideal Coordinates CCD File 
B [auth A]methyl cis-4-[2-(benzoylamino)-6-(piperidin-1-ylmethyl)-1H-benzimidazol-1-yl]cyclohexanecarboxylate
C28 H34 N4 O3
NFTRTTWPZBZTLY-ZRZAMGCNSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0UU PDBBind:  4FOC IC50: 3 (nM) from 1 assay(s)
BindingDB:  4FOC IC50: min: 3, max: 54 (nM) from 2 assay(s)
Binding MOAD:  4FOC IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.686α = 90
b = 57.505β = 90
c = 105.432γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



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