Human asparaginyl-tRNA synthetase bound to adenosine 5'-sulfamate

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 

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Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase.

Xie, S.C.Wang, Y.Morton, C.J.Metcalfe, R.D.Dogovski, C.Pasaje, C.F.A.Dunn, E.Luth, M.R.Kumpornsin, K.Istvan, E.S.Park, J.S.Fairhurst, K.J.Ketprasit, N.Yeo, T.Yildirim, O.Bhebhe, M.N.Klug, D.M.Rutledge, P.J.Godoy, L.C.Dey, S.De Souza, M.L.Siqueira-Neto, J.L.Du, Y.Puhalovich, T.Amini, M.Shami, G.Loesbanluechai, D.Nie, S.Williamson, N.Jana, G.P.Maity, B.C.Thomson, P.Foley, T.Tan, D.S.Niles, J.C.Han, B.W.Goldberg, D.E.Burrows, J.Fidock, D.A.Lee, M.C.S.Winzeler, E.A.Griffin, M.D.W.Todd, M.H.Tilley, L.

(2024) Nat Commun 15: 937-937

  • DOI: https://doi.org/10.1038/s41467-024-45224-z
  • Primary Citation of Related Structures:  
    8H53, 8TC7, 8TC8, 8TC9

  • PubMed Abstract: 

    Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.

  • Organizational Affiliation

    Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Asparagine--tRNA ligase, cytoplasmic
A, B, C, D
548Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43776 (Homo sapiens)
Explore O43776 
Go to UniProtKB:  O43776
PHAROS:  O43776
GTEx:  ENSG00000134440 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43776
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NSS (Subject of Investigation/LOI)
Query on NSS

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B],
U [auth C],
Y [auth D]
C14 H21 N8 O8 S
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
AA [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
V [auth C],
W [auth C],
Z [auth D]
C3 H8 O3
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D],
L [auth A],
T [auth B],
X [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.851α = 90
b = 126.285β = 90
c = 160.598γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

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)AustraliaAPP1171794

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Database references