3RDP

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-METHYL-FHBT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.

Martic, M.Pernot, L.Westermaier, Y.Perozzo, R.Kraljevic, T.G.Kristafor, S.Raic-Malic, S.Scapozza, L.Ametamey, S.

(2011) Nucleosides Nucleotides Nucleic Acids 30: 293-315

  • DOI: 10.1080/15257770.2011.581258
  • Primary Citation of Related Structures:  3F0T
  • Also Cited By: 4IVP, 4IVQ, 4IVR, 4JBX, 4JBY

  • PubMed Abstract: 
  • Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT ...

    Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT), is phosphorylated at a similar rate compared to "gold standard" 9-[4-fluoro-3-(hydroxymethyl)butyl]guanine, FHBG, (K(m) = 10 ± 0.3 μM; k(cat) = 0.036 ± 0.015 sec(-1)). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.


    Related Citations: 
    • Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography.
      Vogt, J.,Perozzo, R.,Pautsch, A.,Prota, A.,Schelling, P.,Pilger, B.,Folkers, G.,Scapozza, L.,Schulz, G.E.
      (2000) Proteins 41: 545


    Organizational Affiliation

    Center for Pharmaceutical Science of ETH, PSI and USZ, ETH Zurich, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidine kinase
A, B
331Human herpesvirus 1 (strain 17)Gene Names: TK
EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17))
Go to UniProtKB:  P03176
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NMF
Query on NMF

Download SDF File 
Download CCD File 
A, B
6-[(2R)-2-(fluoromethyl)-3-hydroxy-propyl]-1,5-dimethyl-pyrimidine-2,4-dione
C10 H15 F N2 O3
OHXHFKXQCMBBKV-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 114.187α = 90.00
b = 118.283β = 90.00
c = 108.871γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Structure summary