8TYF | pdb_00008tyf

Plasmodium vivax PMV-WM06 inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-activity analysis of imino-pyrimidinone-fused pyrrolidines aids the development of dual plasmepsin V and plasmepsin X inhibitors.

Hodder, A.N.Sleebs, B.E.Adams, G.Rezazadeh, S.Ngo, A.Jarman, K.Scally, S.Czabotar, P.Wang, H.McCauley, J.A.Olsen, D.B.Cowman, A.F.

(2025) FEBS J 292: 2843-2864

  • DOI: https://doi.org/10.1111/febs.70038
  • Primary Citation Related Structures: 
    8TYF, 8TYG, 8TYH

  • PubMed Abstract: 

    A library of known aspartic protease inhibitors was screened to identify compounds that inhibit plasmepsin V from Plasmodium vivax. This screen revealed compounds with an imino-pyrimidinone-fused pyrrolidine (IPF) scaffold that exhibited sub-micromolar inhibitory activity against plasmepsin V. Further screening of IPF analogs against the related aspartic protease plasmepsin X showed inhibitory activity, while a third aspartic protease, plasmepsin IX, was not significantly inhibited. Modifications to the P1 biaryl region of the IPF scaffold differentially modulated inhibition of both plasmepsin V and X. Notably, analogs with potent plasmepsin X inhibitory activity successfully blocked the growth of Plasmodium falciparum in vitro. X-ray structures of IPF analogs in complex with plasmepsin V provided insights into their binding mode and revealed avenues to further improve IPF potency and selectivity between plasmepsin V and X. This understanding of how these compounds interact with the active sites of plasmepsin V and X will serve as a foundation for the future design of dual inhibitors targeting these proteases.


  • Organizational Affiliation
    • The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.

Macromolecule Content 

  • Total Structure Weight: 53.65 kDa 
  • Atom Count: 3,338 
  • Modeled Residue Count: 400 
  • Deposited Residue Count: 461 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasmepsin V461Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PMVPVX_116695
EC: 3.4.23
UniProt
Find proteins for A5K302 (Plasmodium vivax (strain Salvador I))
Explore A5K302 
Go to UniProtKB:  A5K302
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K302
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.72α = 90
b = 81.85β = 90
c = 192.876γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-09-10
    Changes: Database references