2XX3

HUMAN THYMIDYLATE KINASE COMPLEXED WITH thymidine butenyl phosphonate monophosphate and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Novel Antiviral C5-Substituted Pyrimidine Acyclic Nucleoside Phosphonates Selected as Human Thymidylate Kinase Substrates.

Topalis, D.Pradere, U.Roy, V.Caillat, C.Azzouzi, A.Broggi, J.Snoeck, R.Andrei, G.Lin, J.Eriksson, S.Alexandre, J.A.C.El-Amri, C.Deville-Bonne, D.Meyer, P.Balzarini, J.Agrofoglio, L.A.

(2011) J.Med.Chem. 54: 222

  • DOI: 10.1021/jm1011462

  • PubMed Abstract: 
  • Acyclic nucleoside phosphonates (ANPs) are at the cornerstone of DNA virus and retrovirus therapies. They reach their target, the viral DNA polymerase, after two phosphorylation steps catalyzed by cellular kinases. New pyrimidine ANPs have been synth ...

    Acyclic nucleoside phosphonates (ANPs) are at the cornerstone of DNA virus and retrovirus therapies. They reach their target, the viral DNA polymerase, after two phosphorylation steps catalyzed by cellular kinases. New pyrimidine ANPs have been synthesized with unsaturated acyclic side chains (prop-2-enyl-, but-2-enyl-, pent-2-enyl-) and different substituents at the C5 position of the uracil nucleobase. Several derivatives in the but-2-enyl- series 9d and 9e, with (E) but not with (Z) configuration, were efficient substrates for human thymidine monophosphate (TMP) kinase, but not for uridine monophosphate-cytosine monophosphate (UMP-CMP) kinase, which is in contrast to cidofovir. Human TMP kinase was successfully crystallized in a complex with phosphorylated (E)-thymidine-but-2-enyl phosphonate 9e and ADP. The bis-pivaloyloxymethyl (POM) esters of (E)-9d and (E)-9e were synthesized and shown to exert activity against herpes virus in vitro (IC(50) = 3 μM) and against varicella zoster virus in vitro (IC(50) = 0.19 μM), in contrast to the corresponding inactive (Z) derivatives. Thus, their antiviral activity correlates with their ability to act as thymidylate kinase substrates.


    Organizational Affiliation

    Groupe d'Enzymologie Moléculaire et Fonctionnelle, UR4-UPMC, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE KINASE
A
232Homo sapiensMutation(s): 0 
Gene Names: DTYMK (CDC8, TMPK, TYMK)
EC: 2.7.4.9
Find proteins for P23919 (Homo sapiens)
Go to Gene View: DTYMK
Go to UniProtKB:  P23919
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAE
Query on TAE

Download SDF File 
Download CCD File 
A
N1-[(E)-4-DIHYDROXYPHOSPHONYL-BUT-2-ENYL]-THYMINE
C9 H14 N2 O8 P2
XCVLZXXLVNRCHX-NSCUHMNNSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.440α = 90.00
b = 38.320β = 123.07
c = 73.160γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-11-08 
  • Released Date: 2011-12-07 
  • Deposition Author(s): Caillat, C., Meyer, P.

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release