1KIM

CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH DEOXYTHYMIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.

Champness, J.N.Bennett, M.S.Wien, F.Visse, R.Summers, W.C.Herdewijn, P.de Clerq, E.Ostrowski, T.Jarvest, R.L.Sanderson, M.R.

(1998) Proteins 32: 350-361

  • DOI: 10.1002/(sici)1097-0134(19980815)32:3<350::aid-prot10>3.0.co;2-8
  • Primary Citation of Related Structures:  
    1KIM, 1KI6, 1KI4, 1KI3, 1KI2, 1KI8, 1KI7

  • PubMed Abstract: 
  • Antiherpes therapies are principally targeted at viral thymidine kinases and utilize nucleoside analogs, the triphosphates of which are inhibitors of viral DNA polymerase or result in toxic effects when incorporated into DNA. The most frequently used ...

    Antiherpes therapies are principally targeted at viral thymidine kinases and utilize nucleoside analogs, the triphosphates of which are inhibitors of viral DNA polymerase or result in toxic effects when incorporated into DNA. The most frequently used drug, aciclovir (Zovirax), is a relatively poor substrate for thymidine kinase and high-resolution structural information on drugs and other molecules binding to the target is therefore important for the design of novel and more potent chemotherapy, both in antiherpes treatment and in gene therapy systems where thymidine kinase is expressed. Here, we report for the first time the binary complexes of HSV-1 thymidine kinase (TK) with the drug molecules aciclovir and penciclovir, determined by X-ray crystallography at 2.37 A resolution. Moreover, from new data at 2.14 A resolution, the refined structure of the complex of TK with its substrate deoxythymidine (R = 0.209 for 96% of all data) now reveals much detail concerning substrate and solvent interactions with the enzyme. Structures of the complexes of TK with four halogen-containing substrate analogs have also been solved, to resolutions better than 2.4 A. The various TK inhibitors broadly fall into three groups which together probe the space of the enzyme active site in a manner that no one molecule does alone, so giving a composite picture of active site interactions that can be exploited in the design of novel compounds.


    Related Citations: 
    • 3'-Amino Thymidine Affinity Matrix for the Purification of Herpes Simplex Virus Thymidine Kinase
      Tung, P.P., Respass, J., Summers, W.C.
      (1996) Yale J Biol Med 69: 495
    • 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 Biol 2: 876
    • The Complete DNA Sequence of the Long Unique Region in the Genome of Herpes Simplex Virus Type 1
      Mcgeoch, D.J., Dalrymple, M.A., Davison, A.J., Dolan, A., Frame, M.C., Mcnab, D., Perry, L.J., Scott, J.E., Taylor, P.
      (1988) J Gen Virol 69: 1531
    • Purification and Crystallization of Thymidine Kinase from Herpes Simplex Virus Type 1
      Sanderson, M.R., Freemont, P.S., Murthy, H.M., Krane, J.F., Summers, W.C., Steitz, T.A.
      (1988) J Mol Biol 202: 917
    • Nucleotide Sequence of the Thymidine Kinase Gene of Herpes Simplex Virus Type 1
      Wagner, M.J., Sharp, J.A., Summers, W.C.
      (1981) Proc Natl Acad Sci U S A 78: 1441

    Organizational Affiliation

    Division of Biomedical Sciences, Randall Institute, King's College, London, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDINE KINASEAB366Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: TKUL23
EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17))
Explore P03176 
Go to UniProtKB:  P03176
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
THM
Query on THM

Download CCD File 
A, B
THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
THM-TΔS:  50.09000015258789   kJ/mol  BindingDB
THMΔH:  79.91000366210938   kJ/mol  BindingDB
THM-TΔS:  36.880001068115234   kJ/mol  BindingDB
THMΔH:  73.08000183105469   kJ/mol  BindingDB
THMΔG:  29.81999969482422   kJ/mol  BindingDB
THMΔG:  29.399999618530273   kJ/mol  BindingDB
THM-TΔS:  27.18000030517578   kJ/mol  BindingDB
THMΔH:  66.36000061035156   kJ/mol  BindingDB
THMΔG:  30.239999771118164   kJ/mol  BindingDB
THMΔH:  57.119998931884766   kJ/mol  BindingDB
THMIC50:  1000   nM  BindingDB
THM-TΔS:  42.79999923706055   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.4α = 90
b = 116.6β = 90
c = 108.2γ = 90
Software Package:
Software NamePurpose
SOLOMONphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance