Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 63.71 kDa 
• Atom Count: 3545 
• Modelled Residue Count: 419 
• Deposited Residue Count: 543 
• Unique protein chains: 1

3T60

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

• PDB DOI: 10.2210/pdb3T60/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

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 
• DOI: 10.1002/cmdc.201100255
• Primary Citation of Related Structures:  
  3T60, 3T64, 3T6Y, 3T70


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative	A, B, C	181	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF11_0282, PF3D7_1127100 EC: 3.6.1.23
UniProt
Find proteins for Q8II92 (Plasmodium falciparum (isolate 3D7)) Explore Q8II92  Go to UniProtKB:  Q8II92

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUA	D [auth A], F [auth B], H [auth C]	2',5'-dideoxy-5'-(tritylamino)uridine C28 H27 N3 O4 TUZNCXRMWDUVNX-BFLUCZKCSA-N
GOL	E [auth A], G [auth B], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DUA	Binding MOAD:  3T60	Ki: 200 (nM) from 1 assay(s)
	BindingDB:  3T60	Ki: 200 (nM) from 1 assay(s)
	PDBBind:  3T60	Ki: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.972	α = 90
b = 76.972	β = 90
c = 106.924	γ = 90

Software Package:

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

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