The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.

Dufe, V.T.Qiu, W.Muller, I.B.Hui, R.Walter, R.D.Al-Karadaghi, S.

(2007) J Mol Biol 373: 167-177

  • DOI: https://doi.org/10.1016/j.jmb.2007.07.053
  • Primary Citation of Related Structures:  
    2I7C, 2PSS, 2PT6, 2PT9

  • PubMed Abstract: 

    Plasmodium falciparum is the causative agent of the most severe type of malaria, a life-threatening disease affecting the lives of over three billion people. Factors like widespread resistance against available drugs and absence of an effective vaccine are seriously compounding control of the malaria parasite. Thus, there is an urgent need for the identification and validation of new drug targets. The enzymes of the polyamine biosynthesis pathway have been suggested as possible targets for the treatment of malaria. One of these enzymes is spermidine synthase (SPDS, putrescine aminopropyltransferase), which catalyzes the transfer of an aminopropyl moiety from decarboxylated S-adenosylmethionine (dcAdoMet) to putrescine, leading to the formation of spermidine and 5'-methylthioadenosine. Here we present the three-dimensional structure of P. falciparum spermidine synthase (pfSPDS) in apo form, in complex with dcAdoMet and two inhibitors, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and trans-4-methylcyclohexylamine (4MCHA). The results show that binding of dcAdoMet to pfSPDS stabilizes the conformation of the flexible gatekeeper loop of the enzyme and affects the conformation of the active-site amino acid residues, preparing the protein for binding of the second substrate. The complexes of AdoDATO and 4MCHA with pfSPDS reveal the mode of interactions of these compounds with the enzyme. While AdoDATO essentially fills the entire active-site pocket, 4MCHA only occupies part of it, which suggests that simple modifications of this compound may yield more potent inhibitors of pfSPDS.

  • Organizational Affiliation

    Department of Molecular Biophysics, Center for Molecular Protein Science, Lund University, S-221 00 Lund, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine synthase
A, B, C
321Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF11_0301
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7))
Explore Q8II73 
Go to UniProtKB:  Q8II73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8II73
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on S4M

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
I [auth C]
C14 H24 N6 O3 S
Query on 1PG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C]
C11 H24 O6
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.3α = 90
b = 134.18β = 94.38
c = 48.32γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Advisory, Data collection, Structure summary
  • Version 1.3: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description