Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63707.86 
• Atom Count: 3449 
• Residue Count: 543 
• Unique protein chains: 1

3T60

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

• DOI: 10.2210/pdb3T60/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum (isolate 3D7)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-07-28 Released: 2012-08-29 
• Deposition Author(s): Hampton, S.E., Baragana, B., Schipani, A., Bosch-Navarrete, C., Musso-Buendia, A., Recio, E., Kaiser, M., Whittingham, J.L., Roberts, S.M., Shevtsov, M., Brannigan, J.A., Kahnberg, P., Brun, R., Wilson, K.S., Gonzalez-Pacanowska, D., Johansson, N.G., Gilbert, I.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.396 Å
• R-Value Free: 0.254 
• R-Value Work: 0.196 

Literature

Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.

Hampton, S.E., Baragana, B., Schipani, A., Bosch-Navarrete, C., Musso-Buendia, J.A., Recio, E., Kaiser, M., Whittingham, J.L., Roberts, S.M., Shevtsov, M., Brannigan, J.A., Kahnberg, P., Brun, R., Wilson, K.S., Gonzalez-Pacanowska, D., Johansson, N.G., Gilbert, I.H.

(2011) Chemmedchem 6: 1816-1831

• PubMed: 22049550 
• Primary Citation of Related Structures:  
  3T64, 3T70, 3T6Y


• PubMed Abstract: 
  

Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is a potential drug target for malaria. We previously reported some 5'-tritylated deoxyuridine analogues (both cyclic and acyclic) as selective inhibitors of the Plasmodium falciparum dUTPase. Modelling studies indicated that it might be possible to replace the trityl group with a diphenyl moiety, as two of the phenyl groups are buried, whereas the third is exposed to solvent. Herein we report the synthesis and evaluation of some diphenyl analogues that have lower lipophilicity and molecular weight than the trityl lead compound. Co-crystal structures show that the diphenyl inhibitors bind in a similar manner to the corresponding trityl derivatives, with the two phenyl moieties occupying the predicted buried phenyl binding sites. The diphenyl compounds prepared show similar or slightly lower inhibition of PfdUTPase, and similar or weaker inhibition of parasite growth than the trityl compounds.

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Organizational Affiliation: 

Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Sir James Black Centre, Dundee DD1 5EH, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative	A, B, C	181	Plasmodium falciparum (isolate 3D7)	Mutation(s): 0  EC: 3.6.1.23
Find proteins for Q8II92 (Plasmodium falciparum (isolate 3D7)) Go to UniProtKB:  Q8II92

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B, C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DUA	A, B, C	2',5'-dideoxy-5'-(tritylamino)uridine C28 H27 N3 O4 TUZNCXRMWDUVNX-BFLUCZKCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DUA	Ki: 200 nM (100) BINDINGDB
DUA	Ki: 1800 nM BINDINGMOAD
DUA	Ki: 200 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.396 Å
• R-Value Free: 0.254 
• R-Value Work: 0.196 
• Space Group: P 4₁

Unit Cell:

Length (Å)	Angle (°)
a = 76.972	α = 90.00
b = 76.972	β = 90.00
c = 106.924	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
ADSC	data collection
SCALEPACK	data scaling
REFMAC	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-28 
• Released Date: 2012-08-29 
• Deposition Author(s): Hampton, S.E., Baragana, B., Schipani, A., Bosch-Navarrete, C., Musso-Buendia, A., Recio, E., Kaiser, M., Whittingham, J.L., Roberts, S.M., Shevtsov, M., Brannigan, J.A., Kahnberg, P., Brun, R., Wilson, K.S., Gonzalez-Pacanowska, D., Johansson, N.G., Gilbert, I.H.

Revision History 

• Version 1.0: 2012-08-29
  Type: Initial release