4DCE

Crystal structure of human anaplastic lymphoma kinase in complex with a piperidine-carboxamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rapid development of piperidine carboxamides as potent and selective anaplastic lymphoma kinase inhibitors.

Bryan, M.C.Whittington, D.A.Doherty, E.M.Falsey, J.R.Cheng, A.C.Emkey, R.Brake, R.L.Lewis, R.T.

(2012) J Med Chem 55: 1698-1705

  • DOI: 10.1021/jm201565s
  • Primary Citation of Related Structures:  
    4DCE

  • PubMed Abstract: 
  • Piperidine carboxamide 1 was identified as a novel inhibitor of anaplastic lymphoma kinase (ALK enzyme assay IC(50) = 0.174 μM) during high throughput screening, with selectivity over the related kinase insulin-like growth factor-1 (IGF1R). The X-ray ...

    Piperidine carboxamide 1 was identified as a novel inhibitor of anaplastic lymphoma kinase (ALK enzyme assay IC(50) = 0.174 μM) during high throughput screening, with selectivity over the related kinase insulin-like growth factor-1 (IGF1R). The X-ray cocrystal structure of 1 with the ALK kinase domain revealed an unusual DFG-shifted conformation, allowing access to an extended hydrophobic pocket. Structure-activity relationship (SAR) studies were focused on the rapid parallel optimization of both the right- and left-hand side of the molecule, culminating in molecules with improved potency and selectivity over IGF1R.


    Organizational Affiliation

    Medicinal Chemistry Research Technologies, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALK tyrosine kinase receptorA, B333Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0JF
Query on 0JF

Download CCD File 
A, B
(3S)-N-(4-methylbenzyl)-1-{2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}piperidine-3-carboxamide
C27 H33 N5 O4
BAQAWVMHTOQJCI-FQEVSTJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0JFIC50:  384   nM  BindingDB
0JFIC50:  174   nM  BindingDB
0JFIC50 :  174   nM  PDBBind
0JFIC50:  174   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.612α = 90
b = 104.819β = 90.15
c = 57.817γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description