8W10 | pdb_00008w10

Plasmodium vivax PMX-MK7602 inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

MK-7602: a potent multi-stage dual-targeting antimalarial.

Favuzza, P.Palandri, J.de Lera Ruiz, M.Bailey, W.Boyce, C.W.Danziger, A.Fawaz, M.V.Kelly, M.Murgolo, N.Robbins, J.A.Vavrek, M.Zhao, L.Lei, Z.Guo, Z.Reaksudsan, K.Steel, R.W.J.Hodder, A.N.Ngo, A.Dziekan, J.M.Thompson, J.K.Triglia, T.Birkinshaw, R.W.Penington, J.S.Scally, S.W.Dans, M.G.Coyle, R.Sevilleno, N.Orban, A.Feufack-Donfack, L.B.Popovici, J.Lee, M.C.S.Papenfuss, A.Lowes, K.N.Sleebs, B.E.McCarthy, J.S.McCauley, J.A.Boddey, J.A.Olsen, D.B.Cowman, A.F.

(2026) EBioMedicine 123: 106061-106061

  • DOI: https://doi.org/10.1016/j.ebiom.2025.106061
  • Primary Citation of Related Structures:  
    8W10

  • PubMed Abstract: 

    The global burden of malaria remains substantial, and increasing parasite resistance to current antimalarials necessitates the development of drugs with unique mechanisms of action. This study aimed to develop and characterise a new antimalarial compound targeting Plasmodium aspartic proteases. We conducted high-throughput screening, medicinal chemistry optimisation, and extensive in vitro and in vivo testing to develop and evaluate MK-7602, a dual inhibitor of plasmepsins IX and X. MK-7602, a clinical candidate, acts as a dual sub-nanomolar inhibitor of plasmepsins IX and X in multiple Plasmodium species. It exhibits favourable pharmacokinetic properties and a promising safety profile. MK-7602 demonstrates activity against liver and blood life-cycle stages of the parasite and blocks transmission to mosquitoes. Importantly, it shows a high barrier to resistance development and lacks cross-resistance with Plasmodium falciparum strains resistant to other antimalarials. MK-7602 effectively inhibits both wild-type parasites and those with increased plasmepsin expression, highlighting its potential to overcome existing resistance mechanisms. MK-7602 represents a new class of antimalarial for treating uncomplicated malaria with a new mechanism of action and the potential to address drug-resistant malaria. Clinical evaluation of MK-7602's activity against P. falciparum is ongoing. This work was funded by The Wellcome Trust (109662/Z/15/Z, 202749/Z/16/Z, 219658/Z/19/Z), NHMRC (GNT1176955, GNT637406, GNT1173049), the Human Frontiers Science Program (LT0001/2022-L, JMD), Drakensberg Trust, the Victorian State Government Operational Infrastructure Support grant, and the Australian Government NHMRC IRIISS. JPo was supported by the NIH/NIAID (R01AI173171, R01AI175134 and R61AI187100) and the Pasteur International Unit PvESMEE.


  • Organizational Affiliation
    • The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; University of Melbourne, Melbourne, 3010, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartyl protease, putative
A, B
379Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_088125
UniProt
Find proteins for A5KAC3 (Plasmodium vivax (strain Salvador I))
Explore A5KAC3 
Go to UniProtKB:  A5KAC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5KAC3
Glycosylation
Glycosylation Sites: 1
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
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZRN (Subject of Investigation/LOI)
Query on ZRN

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
(2R,3S)-3-[(2S)-2-amino-4,4-diethyl-6-oxo-1,3-diazinan-1-yl]-N-[(1R,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-2-(methoxymethyl)-2-methyl-2,3-dihydro-1-benzofuran-5-carboxamide
C29 H36 N4 O5
LREJHMJDUFIXDP-IWNAYQHTSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.31α = 90
b = 88.302β = 90
c = 230.675γ = 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: 2025-02-26
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Database references