6W59

Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC063)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Trypanosoma cruzi Malic Enzyme Is the Target for Sulfonamide Hits from the GSK Chagas Box.

Mercaldi, G.F.Eufrasio, A.G.Ranzani, A.T.do Nascimento Faria, J.Mota, S.G.R.Fagundes, M.Bruder, M.Cordeiro, A.T.

(2021) ACS Infect Dis 7: 2455-2471

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00231
  • Primary Citation of Related Structures:  
    6W29, 6W2N, 6W49, 6W53, 6W56, 6W57, 6W59, 7MF4

  • PubMed Abstract: 

    Chagas disease, an infectious condition caused by Trypanosoma cruzi , lacks treatment with drugs with desired efficacy and safety profiles. To address this unmet medical need, a set of trypanocidal compounds were identified through a large multicenter phenotypic-screening initiative and assembled in the GSK Chagas Box. In the present work, we report the screening of the Chagas Box against T. cruzi malic enzymes (MEs) and the identification of three potent inhibitors of its cytosolic isoform (TcMEc). One of these compounds, TCMDC-143108 ( 1 ), came out as a nanomolar inhibitor of TcMEc, and 14 new derivatives were synthesized and tested for target inhibition and efficacy against the parasite. Moreover, we determined the crystallographic structures of TcMEc in complex with TCMDC-143108 ( 1 ) and six derivatives, revealing the allosteric inhibition site and the determinants of specificity. Our findings connect phenotypic hits from the Chagas Box to a relevant metabolic target in the parasite, providing data to foster new structure-activity guided hit optimization initiatives.


  • Organizational Affiliation

    Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP 13083-970, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malic enzyme554Trypanosoma cruziMutation(s): 0 
Gene Names: C3747_11g406
UniProt
Find proteins for Q4DJ68 (Trypanosoma cruzi (strain CL Brener))
Explore Q4DJ68 
Go to UniProtKB:  Q4DJ68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4DJ68
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SZD (Subject of Investigation/LOI)
Query on SZD

Download Ideal Coordinates CCD File 
C [auth A]3,5-bis(fluoranyl)-~{N}-[3-[[4-(trifluoromethyloxy)phenyl]sulfamoyl]phenyl]benzamide
C20 H13 F5 N2 O4 S
VSBQYLPAMTYZNU-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
B [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.385α = 90
b = 73.385β = 90
c = 233.769γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil16/14271-4
Sao Paulo Research Foundation (FAPESP)Brazil18/22202-8
Sao Paulo Research Foundation (FAPESP)Brazil16/03151-8

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description