8GCC

T. cruzi topoisomerase II alpha bound to dsDNA and the covalent inhibitor CT1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cyanotriazoles are selective topoisomerase II poisons that rapidly cure trypanosome infections.

Rao, S.P.S.Gould, M.K.Noeske, J.Saldivia, M.Jumani, R.S.Ng, P.S.Rene, O.Chen, Y.L.Kaiser, M.Ritchie, R.Francisco, A.F.Johnson, N.Patra, D.Cheung, H.Deniston, C.Schenk, A.D.Cortopassi, W.A.Schmidt, R.S.Wiedemar, N.Thomas, B.Palkar, R.Ghafar, N.A.Manoharan, V.Luu, C.Gable, J.E.Wan, K.F.Myburgh, E.Mottram, J.C.Barnes, W.Walker, J.Wartchow, C.Aziz, N.Osborne, C.Wagner, J.Sarko, C.Kelly, J.M.Manjunatha, U.H.Maeser, P.Jiricek, J.Lakshminarayana, S.B.Barrett, M.P.Diagana, T.T.

(2023) Science 380: 1349-1356

  • DOI: https://doi.org/10.1126/science.adh0614
  • Primary Citation of Related Structures:  
    8GCC

  • PubMed Abstract: 

    Millions who live in Latin America and sub-Saharan Africa are at risk of trypanosomatid infections, which cause Chagas disease and human African trypanosomiasis (HAT). Improved HAT treatments are available, but Chagas disease therapies rely on two nitroheterocycles, which suffer from lengthy drug regimens and safety concerns that cause frequent treatment discontinuation. We performed phenotypic screening against trypanosomes and identified a class of cyanotriazoles (CTs) with potent trypanocidal activity both in vitro and in mouse models of Chagas disease and HAT. Cryo-electron microscopy approaches confirmed that CT compounds acted through selective, irreversible inhibition of trypanosomal topoisomerase II by stabilizing double-stranded DNA:enzyme cleavage complexes. These findings suggest a potential approach toward successful therapeutics for the treatment of Chagas disease.


  • Organizational Affiliation

    Novartis Institute for Tropical Diseases, Emeryville, CA, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 2
A, B
779Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: Tc00.1047053508699.10
EC: 5.6.2.2
UniProt
Find proteins for Q4DE53 (Trypanosoma cruzi (strain CL Brener))
Explore Q4DE53 
Go to UniProtKB:  Q4DE53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4DE53
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (28-MER)
C, D
28Escherichia coli
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YWX (Subject of Investigation/LOI)
Query on YWX

Download Ideal Coordinates CCD File 
E [auth C],
F [auth D]
2-{3-[(Z)-iminomethyl]-1H-1,2,4-triazol-1-yl}-1-{(3M)-3-[2-(trifluoromethyl)phenyl]-6H-pyrrolo[3,4-b]pyridin-6-yl}ethan-1-one
C19 H13 F3 N6 O
CZMOUVMERVDBNS-OUBWWKSTSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom219639/Z/19/Z
Wellcome TrustUnited Kingdom108517/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary