8TYG | pdb_00008tyg

Plasmodium vivax PMV-WM08 inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8TYG

Ligand Structure Quality Assessment 


This is version 1.3 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: 55.75 kDa 
  • Atom Count: 3,753 
  • Modeled Residue Count: 405 
  • 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: 3
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TEW

Query on TEW



Download:Ideal Coordinates CCD File
D [auth A]6-tungstotellurate(VI)
O24 Te W6
JDLYBIMRCSJRQJ-UHFFFAOYSA-M
SKC
(Subject of Investigation/LOI)

Query on SKC



Download:Ideal Coordinates CCD File
C [auth A](2E,4aR,7aS)-6-[3-(4-chlorophenyl)pyridin-2-yl]-7a-(2,5-difluorophenyl)-2-imino-3-methyloctahydro-4H-pyrrolo[3,4-d]pyrimidin-4-one
C24 H20 Cl F2 N5 O
JZQJSLYBFWXABF-YADARESESA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.772α = 90
b = 86.994β = 90
c = 192.463γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2024-12-25
    Changes: Advisory, Derived calculations, Structure summary
  • Version 1.2: 2025-03-26
    Changes: Database references
  • Version 1.3: 2025-06-18
    Changes: Database references