5EQE

Crystal structure of choline kinase alpha-1 bound by [4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine (compound 11)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 

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Ligand Structure Quality Assessment 


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 antiproliferative activity in both cellular and animal models, this novel oncogene has recently gained interest as a promising small molecule target for cancer therapy ...

    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 alphaA, B401Homo sapiensMutation(s): 0 
Gene Names: CHKACHKCKI
EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P35790 (Homo sapiens)
Explore P35790 
Go to UniProtKB:  P35790
PHAROS:  P35790
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5R8 (Subject of Investigation/LOI)
Query on 5R8

Download Ideal Coordinates CCD File 
C [auth A], D [auth B][4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine
C14 H23 N3
AQLZGQUKWNQYPH-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5R8 BindingDB:  5EQE Kd: 1.32e+5 (nM) from 1 assay(s)
IC50: 8.70e+4 (nM) from 1 assay(s)
Binding MOAD:  5EQE Kd: 1.32e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.671α = 90
b = 120.878β = 90
c = 131.208γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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