6C4G

Plasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-601)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Enhanced antimalarial activity of plasmepsin V inhibitors by modification of the P2position of PEXEL peptidomimetics.

Nguyen, W.Hodder, A.N.de Lezongard, R.B.Czabotar, P.E.Jarman, K.E.O'Neill, M.T.Thompson, J.K.Jousset Sabroux, H.Cowman, A.F.Boddey, J.A.Sleebs, B.E.

(2018) Eur J Med Chem 154: 182-198

  • DOI: https://doi.org/10.1016/j.ejmech.2018.05.022
  • Primary Citation of Related Structures:  
    6C4G

  • PubMed Abstract: 

    Plasmepsin V is an aspartyl protease that plays a critical role in the export of proteins bearing the Plasmodium export element (PEXEL) motif (RxLxQ/E/D) to the infected host erythrocyte, and thus the survival of the malaria parasite. Previously, development of transition state PEXEL mimetic inhibitors of plasmepsin V have primarily focused on demonstrating the importance of the P 3 Arg and P 1 Leu in binding affinity and selectivity. Here, we investigate the importance of the P 2 position by incorporating both natural and non-natural amino acids into this position and show disubstituted beta-carbon amino acids convey the greatest potency. Consequently, we show analogues with either cyclohexylglycine or phenylglycine in the P 2 position are the most potent inhibitors of plasmepsin V that impair processing of the PEXEL motif in exported proteins resulting in death of P. falciparum asexual stage parasites.


  • Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartic protease PM5444Plasmodium vivaxMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EQG (Subject of Investigation/LOI)
Query on EQG

Download Ideal Coordinates CCD File 
D [auth A]benzyl [(6S,7S,10S,13S,18Z)-18-amino-10-cyclohexyl-6-hydroxy-18-imino-7-(2-methylpropyl)-4,9,12-trioxo-1-phenyl-16-oxa-3,8,11,17-tetraazaoctadecan-13-yl]carbamate
C37 H55 N7 O7
QUXHBSKCTRDCOH-QUUJSONZSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EQG Binding MOAD:  6C4G IC50: 5 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.541α = 90
b = 91.192β = 90
c = 176.038γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1113712
National Health and Medical Research Council (NHMRC, Australia)Australia121178
National Health and Medical Research Council (NHMRC, Australia)Australia1117288
National Health and Medical Research Council (NHMRC, Australia)Australia1092789
National Health and Medical Research Council (NHMRC, Australia)Australia1079700
CASS Foundation Science and Medicine GrantAustraliaSM/15/6430

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary