3F0T

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with N-methyl-DHBT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  
  • Also Cited By: 4JBY, 4JBX, 4IVR, 4IVQ, 4IVP

  • 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
    • The three-dimensional structure of thymidine kinase from herpes simplex virus type 1.
      Wild, K.,Bohner, T.,Aubry, A.,Folkers, G.,Schulz, G.E.
      (1995) Febs Lett. 368: 289
    • Crystal structures of the thymidine kinase from herpes simplex virus type-1 in complex with deoxythymidine and ganciclovir.
      Brown, D.G.,Visse, R.,Sandhu, G.,Davies, A.,Rizkallah, P.J.,Melitz, C.,Summers, W.C.,Sanderson, M.R.
      (1995) Nat.Struct.Mol.Biol. 2: 876


    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
332Human herpesvirus 1 (strain 17)Mutation(s): 0 
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
NCV
Query on NCV

Download SDF File 
Download CCD File 
A, B
N-Methyl-6-(1,3-dihydroxy-isobutyl)thymine
6-[3-hydroxy-2-(hydroxymethyl)propyl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione, N-methyl-DHBT
C10 H16 N2 O4
FMPCUJIPAJPVKR-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 113.000α = 90.00
b = 117.365β = 90.00
c = 107.762γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-03
    Type: Database references
  • Version 1.3: 2013-10-02
    Type: Structure summary