4ZL4

Plasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-842)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis for plasmepsin V inhibition that blocks export of malaria proteins to human erythrocytes.

Hodder, A.N.Sleebs, B.E.Czabotar, P.E.Gazdik, M.Xu, Y.O'Neill, M.T.Lopaticki, S.Nebl, T.Triglia, T.Smith, B.J.Lowes, K.Boddey, J.A.Cowman, A.F.

(2015) Nat Struct Mol Biol 22: 590-596

  • DOI: 10.1038/nsmb.3061
  • Primary Citation of Related Structures:  
    4ZL4

  • PubMed Abstract: 
  • Plasmepsin V, an essential aspartyl protease of malaria parasites, has a key role in the export of effector proteins to parasite-infected erythrocytes. Consequently, it is an important drug target for the two most virulent malaria parasites of humans, Plasmodium falciparum and Plasmodium vivax ...

    Plasmepsin V, an essential aspartyl protease of malaria parasites, has a key role in the export of effector proteins to parasite-infected erythrocytes. Consequently, it is an important drug target for the two most virulent malaria parasites of humans, Plasmodium falciparum and Plasmodium vivax. We developed a potent inhibitor of plasmepsin V, called WEHI-842, which directly mimics the Plasmodium export element (PEXEL). WEHI-842 inhibits recombinant plasmepsin V with a half-maximal inhibitory concentration of 0.2 nM, efficiently blocks protein export and inhibits parasite growth. We obtained the structure of P. vivax plasmepsin V in complex with WEHI-842 to 2.4-Å resolution, which provides an explanation for the strict requirements for substrate and inhibitor binding. The structure characterizes both a plant-like fold and a malaria-specific helix-turn-helix motif that are likely to be important in cleavage of effector substrates for export.


    Organizational Affiliation

    1] Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. [2] Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartic protease PM5A, B444Plasmodium vivaxMutation(s): 0 
UniProt
Find proteins for Q6PRR9 (Plasmodium vivax)
Explore Q6PRR9 
Go to UniProtKB:  Q6PRR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PRR9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4PK
Query on 4PK

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
N-[(benzyloxy)carbonyl]-O-carbamimidamido-L-homoseryl-N-{(3S,4S)-3-hydroxy-6-methyl-1-oxo-1-[(2-phenylethyl)amino]heptan-4-yl}-L-valinamide
C34 H51 N7 O7
VAHRPHLZONNTFF-NUISNXNRSA-N
 Ligand Interaction
4PF
Query on 4PF

Download Ideal Coordinates CCD File 
R [auth B](2R)-1-[(2R)-2-(2-methoxyethoxy)propoxy]propan-2-amine
C9 H21 N O3
QZWPAMVDKNPIHV-RKDXNWHRSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
L [auth B],
M [auth B],
D [auth A],
E [auth A],
F [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4PK Binding MOAD:  4ZL4 Kd: 13.8 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.994α = 90
b = 203.089β = 121.07
c = 82.165γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia637406
National Health and Medical Research Council (NHMRC, Australia)Australia1057960
National Health and Medical Research Council (NHMRC, Australia)Australia1010326
Howard Hughes Medical Institute (HHMI)United States55007645

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence