4KW5

M. tuberculosis DprE1 in complex with inhibitor TCA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.612 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of a small molecule with activity against drug-resistant and persistent tuberculosis.

Wang, F.Sambandan, D.Halder, R.Wang, J.Batt, S.M.Weinrick, B.Ahmad, I.Yang, P.Zhang, Y.Kim, J.Hassani, M.Huszar, S.Trefzer, C.Ma, Z.Kaneko, T.Mdluli, K.E.Franzblau, S.Chatterjee, A.K.Johnson, K.Mikusova, K.Besra, G.S.Futterer, K.Jacobs, W.R.Schultz, P.G.

(2013) Proc.Natl.Acad.Sci.USA 110: E2510-E2517

  • DOI: 10.1073/pnas.1309171110

  • PubMed Abstract: 
  • A cell-based phenotypic screen for inhibitors of biofilm formation in mycobacteria identified the small molecule TCA1, which has bactericidal activity against both drug-susceptible and -resistant Mycobacterium tuberculosis (Mtb) and sterilizes Mtb in ...

    A cell-based phenotypic screen for inhibitors of biofilm formation in mycobacteria identified the small molecule TCA1, which has bactericidal activity against both drug-susceptible and -resistant Mycobacterium tuberculosis (Mtb) and sterilizes Mtb in vitro combined with rifampicin or isoniazid. In addition, TCA1 has bactericidal activity against nonreplicating Mtb in vitro and is efficacious in acute and chronic Mtb infection mouse models both alone and combined with rifampicin or isoniazid. Transcriptional analysis revealed that TCA1 down-regulates genes known to be involved in Mtb persistence. Genetic and affinity-based methods identified decaprenyl-phosphoryl-β-D-ribofuranose oxidoreductase DprE1 and MoeW, enzymes involved in cell wall and molybdenum cofactor biosynthesis, respectively, as targets responsible for the activity of TCA1. These in vitro and in vivo results indicate that this compound functions by a unique mechanism and suggest that TCA1 may lead to the development of a class of antituberculosis agents.


    Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxidoreductase
A, B
461N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1W6
Query on 1W6

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Download CCD File 
A, B
ethyl ({2-[(1,3-benzothiazol-2-ylcarbonyl)amino]thiophen-3-yl}carbonyl)carbamate
C16 H13 N3 O4 S2
ISNBJLXHBBZKSL-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.612 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.230α = 90.00
b = 84.190β = 103.55
c = 81.050γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
GDAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references