4L5B

Human dCK C4S-S74E mutant in complex with UDP and the DI-43 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography.

Murphy, J.M.Armijo, A.L.Nomme, J.Lee, C.H.Smith, Q.A.Li, Z.Campbell, D.O.Liao, H.I.Nathanson, D.A.Austin, W.R.Lee, J.T.Darvish, R.Wei, L.Wang, J.Su, Y.Damoiseaux, R.Sadeghi, S.Phelps, M.E.Herschman, H.R.Czernin, J.Alexandrova, A.N.Jung, M.E.Lavie, A.Radu, C.G.

(2013) J.Med.Chem. 56: 6696-6708

  • DOI: 10.1021/jm400457y
  • Primary Citation of Related Structures:  4JLK

  • PubMed Abstract: 
  • Combined inhibition of ribonucleotide reductase and deoxycytidine kinase (dCK) in multiple cancer cell lines depletes deoxycytidine triphosphate pools leading to DNA replication stress, cell cycle arrest, and apoptosis. Evidence implicating dCK in ca ...

    Combined inhibition of ribonucleotide reductase and deoxycytidine kinase (dCK) in multiple cancer cell lines depletes deoxycytidine triphosphate pools leading to DNA replication stress, cell cycle arrest, and apoptosis. Evidence implicating dCK in cancer cell proliferation and survival stimulated our interest in developing small molecule dCK inhibitors. Following a high throughput screen of a diverse chemical library, a structure-activity relationship study was carried out. Positron Emission Tomography (PET) using (18)F-L-1-(2'-deoxy-2'-FluoroArabinofuranosyl) Cytosine ((18)F-L-FAC), a dCK-specific substrate, was used to rapidly rank lead compounds based on their ability to inhibit dCK activity in vivo. Evaluation of a subset of the most potent compounds in cell culture (IC50 = ∼1-12 nM) using the (18)F-L-FAC PET pharmacodynamic assay identified compounds demonstrating superior in vivo efficacy.


    Organizational Affiliation

    Department of Molecular and Medical Pharmacology, §Ahmanson Translational Imaging Division, ⊥Department of Chemistry and Biochemistry, #California NanoSystems Institute, △Department of Biological Chemistry, University of California, Los Angeles , 650 Charles E. Young Dr. S., Los Angeles, California 90095, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidine kinase
A, B
280Homo sapiensGene Names: DCK
EC: 2.7.1.74
Find proteins for P27707 (Homo sapiens)
Go to Gene View: DCK
Go to UniProtKB:  P27707
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
1UX
Query on 1UX

Download SDF File 
Download CCD File 
A, B
1-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]-2-methylpropan-2-ol
C22 H29 N5 O3 S2
PWASXBOUTAWHOZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1UXIC50: 1.4 - 15 nM (98) BINDINGDB
1UXKi: 0.8 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 68.671α = 90.00
b = 68.671β = 90.00
c = 120.019γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata scaling
XDSdata reduction
CrystalCleardata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-10 
  • Released Date: 2013-09-18 
  • Deposition Author(s): Nomme, J., Lavie, A.

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references