4Y6M

Structure of plasmepsin II from Plasmodium falciparum complexed with inhibitor PG418


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


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Literature

Structures of plasmepsin II from Plasmodium falciparum in complex with two hydroxyethylamine-based inhibitors.

Recacha, R.Leitans, J.Akopjana, I.Aprupe, L.Trapencieris, P.Jaudzems, K.Jirgensons, A.Tars, K.

(2015) Acta Crystallogr.,Sect.F 71: 1531-1539

  • DOI: 10.1107/S2053230X15022049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasmepsin II (PMII) is one of the ten plasmepsins (PMs) identified in the genome of Plasmodium falciparum, the causative agent of the most severe and deadliest form of malaria. Owing to the emergence of P. falciparum strains that are resistant to cu ...

    Plasmepsin II (PMII) is one of the ten plasmepsins (PMs) identified in the genome of Plasmodium falciparum, the causative agent of the most severe and deadliest form of malaria. Owing to the emergence of P. falciparum strains that are resistant to current antimalarial agents such as chloroquine and sulfadoxine/pyrimethamine, there is a constant pressure to find new and lasting chemotherapeutic drug therapies. Previously, the crystal structure of PMII in complex with NU655, a potent antimalarial hydroxyethylamine-based inhibitor, and the design of new compounds based on it have been reported. In the current study, two of these newly designed hydroxyethylamine-based inhibitors, PG418 and PG394, were cocrystallized with PMII and their structures were solved, analyzed and compared with that of the PMII-NU655 complex. Structural analysis of the PMII-PG418 complex revealed that the flap loop can adopt a fully closed conformation, stabilized by interactions with the inhibitor, and a fully open conformation, causing an overall expansion in the active-site cavity, which in turn causes unstable binding of the inhibitor. PG418 also stabilizes the flexible loop Gln275-Met286 of another monomer in the asymmetric unit of PMII, which is disordered in the PMII-NU655 complex structure. The crystal structure of PMII in complex with the inhibitor PG418 demonstrates the conformational flexibility of the active-site cavity of the plasmepsins. The interactions of the different moieties in the P1' position of PG418 and PG394 with Thr217 have to be taken into account in the design of new potent plasmepsin inhibitors.


    Related Citations: 
    • Plasmepsin inhibitory activity and structure-guided optimization of a potent hydroxyethylamine-based antimalarial hit.
      Jaudzems, K.,Tars, K.,Maurops, G.,Ivdra, N.,Otikovs, M.,Leitans, J.,Kanepe-Lapsa, I.,Domraceva, I.,Mutule, I.,Trapencieris, P.,Blackman, M.J.,Jirgensons, A.
      (2014) ACS Med Chem Lett 5: 373


    Organizational Affiliation

    Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasmepsin-2
A, B, C
329Plasmodium falciparumMutation(s): 0 
EC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum)
Go to UniProtKB:  P46925
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
48Q
Query on 48Q

Download SDF File 
Download CCD File 
A, B, C
~{N}1-[(~{Z},3~{R})-4-[2-(3-methoxyphenyl)propan-2-ylamino]-3-oxidanyl-1-phenyl-but-1-en-2-yl]-5-piperidin-1-yl-~{N}3,~{N}3-dipropyl-benzene-1,3-dicarboxamide
C39 H52 N4 O4
UCBMZABMPAPJRC-LMOGZCTNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.220α = 90.00
b = 104.600β = 90.00
c = 111.680γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Data collection