Crystal structure of M. tuberculosis DprE1 in complex with sPBTZ169 (sulfonylPBTZ)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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Structure-Based Drug Design and Characterization of Sulfonyl-Piperazine Benzothiazinone Inhibitors of DprE1 from Mycobacterium tuberculosis.

Piton, J.Vocat, A.Lupien, A.Foo, C.S.Riabova, O.Makarov, V.Cole, S.T.

(2018) Antimicrob Agents Chemother 62

  • DOI: https://doi.org/10.1128/AAC.00681-18
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Macozinone (MCZ) is a tuberculosis (TB) drug candidate that specifically targets the essential flavoenzyme DprE1, thereby blocking synthesis of the cell wall precursor decaprenyl phosphoarabinose (DPA) and provoking lysis of Mycobacterium tuberculosis As part of the MCZ backup program, we exploited structure-guided drug design to produce a new series of sulfone-containing derivatives, 2-sulfonylpiperazin 8-nitro 6-trifluoromethyl 1,3-benzothiazin-4-one, or sPBTZ. These compounds are less active than MCZ but have a better solubility profile, and some derivatives display enhanced stability in microsomal assays. DprE1 was efficiently inhibited by sPBTZ, and covalent adducts with the active-site cysteine residue (C387) were formed. However, despite the H-bonding potential of the sulfone group, no additional bonds were seen in the crystal structure of the sPBTZ-DprE1 complex with compound 11326127 compared to MCZ. Compound 11626091, the most advanced sPBTZ, displayed good antitubercular activity in the murine model of chronic TB but was less effective than MCZ. Nonetheless, further testing of this MCZ backup compound is warranted as part of combination treatment with other TB drugs.

  • Organizational Affiliation

    Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Decaprenylphosphoryl-beta-D-ribose oxidase
A, B
481Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: dprE1Rv3790
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJF1 
Go to UniProtKB:  P9WJF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJF1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C27 H33 N9 O15 P2
EQ8 (Subject of Investigation/LOI)
Query on EQ8

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C19 H22 F3 N4 O4 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.164α = 90
b = 84.024β = 103.98
c = 81.666γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European UnionSwitzerland260872

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2023-03-08
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description