5W6O

Choline Kinase Alpha in Complex with TCD-717


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of a Unique Inhibitor-Binding Site on Choline Kinase alpha.

Kall, S.L.Delikatny, E.J.Lavie, A.

(2018) Biochemistry 57: 1316-1325

  • DOI: https://doi.org/10.1021/acs.biochem.7b01257
  • Primary Citation of Related Structures:  
    5W6O

  • PubMed Abstract: 

    Choline kinase α (ChoKα) is an enzyme that is upregulated in many types of cancer and has been shown to be tumorigenic. As such, it makes a promising target for inhibiting tumor growth. Though there have been several inhibitors synthesized for ChoKα, not all of them demonstrate the same efficacy in vivo, though the reasons behind this difference in potency are not clear. One particular inhibitor, designated TCD-717, has recently completed phase I clinical trials. Cell culture and in vitro studies support the powerful inhibitory effect TCD-717 has on ChoKα, but an examination of the inhibitor's interaction with the ChoKα enzyme has been missing prior to this work. Here we detail the 2.35 Å structure of ChoKα in complex with TCD-717. Examination of this structure in conjunction with kinetic assays reveals that TCD-717 does not bind directly in the choline pocket as do previously characterized ChoKα inhibitors, but rather in a proximal but novel location near the surface of the enzyme. The unique binding site identified for TCD-717 lends insight for the future design of more potent in vivo inhibitors for ChoKα.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Choline kinase alpha
A, B
378Homo 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
GTEx:  ENSG00000110721 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35790
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9X1
Query on 9X1

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
1,1'-[[1,1'-biphenyl]-4,4'-diylbis(methylene)]bis{4-[(4-chlorophenyl)(methyl)amino]quinolin-1-ium}
C46 H38 Cl2 N4
QGYGTMZEJNOHNU-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9X1 Binding MOAD:  5W6O IC50: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.95α = 90
b = 122.35β = 90
c = 131.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States4T32DE018381-09

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence