4FOD

Crystal structure of human anaplastic lymphoma kinase in complex with acyliminobenzimidazole inhibitor 36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 ...

    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 receptorA333Homo sapiensMutation(s): 1 
Gene Names: ALK
EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
NIH Common Fund Data Resources
PHAROS  Q9UM73
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0UV
Query on 0UV

Download CCD File 
A
4-fluoro-N-{(2E)-6-{[4-(2-hydroxypropan-2-yl)piperidin-1-yl]methyl}-1-[cis-4-(propan-2-ylcarbamoyl)cyclohexyl]-1,3-dihydro-2H-benzimidazol-2-ylidene}benzamide
C33 H44 F N5 O3
WSTUJEXAPHIEIM-FEGDYQJNSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0UVIC50:  1.2000000476837158   nM  Binding MOAD
0UVIC50 :  1.2000000476837158   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.717α = 90
b = 57.7β = 90
c = 105.939γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-15
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description