8TC8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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:  
    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 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.


Macromolecules
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 
Gene Names: NARS1NARSNRS
EC: 6.1.1.22
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
Expand
  • 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]
5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE
C14 H21 N8 O8 S
MOAVDHSPHZUJSX-UFIIOMENSA-O
GOL
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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D],
L [auth A],
T [auth B],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
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)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