5EQY

Crystal structure of choline kinase alpha-1 bound by 5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile (compound 65)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery.

Zech, S.G.Kohlmann, A.Zhou, T.Li, F.Squillace, R.M.Parillon, L.E.Greenfield, M.T.Miller, D.P.Qi, J.Thomas, R.M.Wang, Y.Xu, Y.Miret, J.J.Shakespeare, W.C.Zhu, X.Dalgarno, D.C.

(2016) J Med Chem 59: 671-686

  • DOI: 10.1021/acs.jmedchem.5b01552
  • Primary Citation of Related Structures:  
    5EQY, 5EQP, 5EQE

  • PubMed Abstract: 
  • Choline kinase α (ChoKα) is an enzyme involved in the synthesis of phospholipids and thereby plays key roles in regulation of cell proliferation, oncogenic transformation, and human carcinogenesis. Since several inhibitors of ChoKα display antiprolif ...

    Choline kinase α (ChoKα) is an enzyme involved in the synthesis of phospholipids and thereby plays key roles in regulation of cell proliferation, oncogenic transformation, and human carcinogenesis. Since several inhibitors of ChoKα display antiproliferative activity in both cellular and animal models, this novel oncogene has recently gained interest as a promising small molecule target for cancer therapy. Here we summarize our efforts to further validate ChoKα as an oncogenic target and explore the activity of novel small molecule inhibitors of ChoKα. Starting from weakly binding fragments, we describe a structure based lead discovery approach, which resulted in novel highly potent inhibitors of ChoKα. In cancer cell lines, our lead compounds exhibit a dose-dependent decrease of phosphocholine, inhibition of cell growth, and induction of apoptosis at low micromolar concentrations. The druglike lead series presented here is optimizable for improvements in cellular potency, drug target residence time, and pharmacokinetic parameters. These inhibitors may be utilized not only to further validate ChoKα as antioncogenic target but also as novel chemical matter that may lead to antitumor agents that specifically interfere with cancer cell metabolism.


    Organizational Affiliation

    ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Choline kinase alphaAB401Homo sapiensMutation(s): 0 
Gene Names: CHKACHKCKI
EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
Find proteins for P35790 (Homo sapiens)
Explore P35790 
Go to UniProtKB:  P35790
NIH Common Fund Data Resources
PHAROS  P35790
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5RA
Query on 5RA

Download CCD File 
A, B
5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile
C27 H37 N5
MJTWJYMXCDQAOT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5RAIC50:  70   nM  Binding MOAD
5RAIC50:  66   nM  BindingDB
5RAKd:  10   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.523α = 90
b = 121.532β = 90
c = 130.467γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
CNXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-06
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Structure summary
  • Version 1.2: 2016-02-10
    Changes: Database references