4JLN

Human dCK C4S-S74E mutant in complex with UDP and the F2.4.1 inhibitor (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-PROPYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules.

Nomme, J.Murphy, J.M.Su, Y.Sansone, N.D.Armijo, A.L.Olson, S.T.Radu, C.Lavie, A.

(2014) Acta Crystallogr.,Sect.D 70: 68-78

  • DOI: 10.1107/S1399004713025030
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Deoxycytidine kinase (dCK) is a key enzyme in the nucleoside salvage pathway that is also required for the activation of several anticancer and antiviral nucleoside analog prodrugs. Additionally, dCK has been implicated in immune disorders and has be ...

    Deoxycytidine kinase (dCK) is a key enzyme in the nucleoside salvage pathway that is also required for the activation of several anticancer and antiviral nucleoside analog prodrugs. Additionally, dCK has been implicated in immune disorders and has been found to be overexpressed in several cancers. To allow the probing and modulation of dCK activity, a new class of small-molecule inhibitors of the enzyme were developed. Here, the structural characterization of four of these inhibitors in complex with human dCK is presented. The structures reveal that the compounds occupy the nucleoside-binding site and bind to the open form of dCK. Surprisingly, a slight variation in the nature of the substituent at the 5-position of the thiazole ring governs whether the active site of the enzyme is occupied by one or two inhibitor molecules. Moreover, this substituent plays a critical role in determining the affinity, improving it from >700 to 1.5 nM in the best binder. These structures lay the groundwork for future modifications that would result in even tighter binding and the correct placement of moieties that confer favorable pharmacodynamics and pharmacokinetic properties.


    Organizational Affiliation

    Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, Chicago, IL 60612, USA.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidine kinase
A, B
280Homo sapiensMutation(s): 5 
Gene 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
18V
Query on 18V

Download SDF File 
Download CCD File 
A, B
2-[({2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-propyl-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine
C20 H24 F N5 O2 S2
FZFMUZLLFBZGTQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
18VKi: 1.5 nM (98) BINDINGDB
18VIC50: 3 nM (98) BINDINGDB
18VKi: 1.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 68.650α = 90.00
b = 68.650β = 90.00
c = 120.050γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CrystalCleardata collection
XDSdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-12 
  • Released Date: 2014-01-22 
  • Deposition Author(s): Nomme, J., Lavie, A.

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references