4KW5 | pdb_00004kw5

M. tuberculosis DprE1 in complex with inhibitor TCA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.247 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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 U S A 110: E2510-E2517

  • DOI: https://doi.org/10.1073/pnas.1309171110
  • Primary Citation Related Structures: 
    4KW5

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 103.11 kDa 
  • Atom Count: 6,565 
  • Modeled Residue Count: 841 
  • Deposited Residue Count: 922 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxidoreductase
A, B
461Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv3790RVBD_3790
EC: 1.1.98.3
UniProt
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
1W6

Query on 1W6



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
ethyl ({2-[(1,3-benzothiazol-2-ylcarbonyl)amino]thiophen-3-yl}carbonyl)carbamate
C16 H13 N3 O4 S2
ISNBJLXHBBZKSL-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
F [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
1W6 BindingDB:  4KW5 IC50: min: 53, max: 266 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.247 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.23α = 90
b = 84.19β = 103.55
c = 81.05γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description