9CLL | pdb_00009cll

Plasmodium falciparum tyrosyl-tRNA synthetase in complex with ML471-Tyr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A potent and selective reaction hijacking inhibitor of Plasmodium falciparum tyrosine tRNA synthetase exhibits single dose oral efficacy in vivo.

Xie, S.C.Tai, C.W.Morton, C.J.Ma, L.Huang, S.C.Wittlin, S.Du, Y.Hu, Y.Dogovski, C.Salimimarand, M.Griffin, R.England, D.de la Cruz, E.Deni, I.Yeo, T.Burkhard, A.Y.Striepen, J.Schindler, K.A.Crespo, B.Gamo, F.J.Khandokar, Y.Hutton, C.A.Rabie, T.Birkholtz, L.M.Famodimu, M.T.Delves, M.J.Bolsher, J.Koolen, K.M.J.van der Laak, R.Aguiar, A.C.C.Pereira, D.B.Guido, R.V.C.Creek, D.J.Fidock, D.A.Dick, L.R.Brand, S.L.Gould, A.E.Langston, S.Griffin, M.D.W.Tilley, L.

(2024) PLoS Pathog 20: e1012429-e1012429

  • DOI: https://doi.org/10.1371/journal.ppat.1012429
  • Primary Citation of Related Structures:  
    9CLL

  • PubMed Abstract: 

    The Plasmodium falciparum cytoplasmic tyrosine tRNA synthetase (PfTyrRS) is an attractive drug target that is susceptible to reaction-hijacking by AMP-mimicking nucleoside sulfamates. We previously identified an exemplar pyrazolopyrimidine ribose sulfamate, ML901, as a potent reaction hijacking inhibitor of PfTyrRS. Here we examined the stage specificity of action of ML901, showing very good activity against the schizont stage, but lower trophozoite stage activity. We explored a series of ML901 analogues and identified ML471, which exhibits improved potency against trophozoites and enhanced selectivity against a human cell line. Additionally, it has no inhibitory activity against human ubiquitin-activating enzyme (UAE) in vitro. ML471 exhibits low nanomolar activity against asexual blood stage P. falciparum and potent activity against liver stage parasites, gametocytes and transmissible gametes. It is fast-acting and exhibits a long in vivo half-life. ML471 is well-tolerated and shows single dose oral efficacy in the SCID mouse model of P. falciparum malaria. We confirm that ML471 is a reaction hijacking inhibitor that is converted into a tight binding Tyr-ML471 conjugate by the PfTyrRS enzyme. A crystal structure of the PfTyrRS/ Tyr-ML471 complex offers insights into improved potency, while molecular docking into UAE provides a rationale for improved selectivity.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tyrosine--tRNA ligase
A, B
373Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0807900
EC: 6.1.1.1
UniProt
Find proteins for Q8IAR7 (Plasmodium falciparum (isolate 3D7))
Explore Q8IAR7 
Go to UniProtKB:  Q8IAR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IAR7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AZG (Subject of Investigation/LOI)
Query on A1AZG

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
{(2R,3S,4R,5R)-5-[4-amino-3-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-dihydroxyoxolan-2-yl}methyl [(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]sulfamate
C22 H29 N7 O8 S
ZOGBAKBFHJWHJQ-DVQOCAJJSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
K [auth B],
L [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.208α = 90
b = 47.271β = 94.628
c = 140.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Global Health Innovative Technology FundJapanH2019-104
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP2022075

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references