5JZB

Crystal structure of HsaD bound to 3,5-dichlorobenzene sulphonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach.

Ryan, A.Polycarpou, E.Lack, N.A.Evangelopoulos, D.Sieg, C.Halman, A.Bhakta, S.Eleftheriadou, O.McHugh, T.D.Keany, S.Lowe, E.D.Ballet, R.Abuhammad, A.Jacobs, W.R.Ciulli, A.Sim, E.

(2017) Br J Pharmacol 174: 2209-2224

  • DOI: https://doi.org/10.1111/bph.13810
  • Primary Citation of Related Structures:  
    5JZ9, 5JZB, 5JZS

  • PubMed Abstract: 

    With the emergence of extensively drug-resistant tuberculosis, there is a need for new anti-tubercular drugs that work through novel mechanisms of action. The meta cleavage product hydrolase, HsaD, has been demonstrated to be critical for the survival of Mycobacterium tuberculosis in macrophages and is encoded in an operon involved in cholesterol catabolism, which is identical in M. tuberculosis and M. bovis BCG. We generated a mutant strain of M. bovis BCG with a deletion of hsaD and tested its growth on cholesterol. Using a fragment based approach, over 1000 compounds were screened by a combination of differential scanning fluorimetry, NMR spectroscopy and enzymatic assay with pure recombinant HsaD to identify potential inhibitors. We used enzymological and structural studies to investigate derivatives of the inhibitors identified and to test their effects on growth of M. bovis BCG and M. tuberculosis. The hsaD deleted strain was unable to grow on cholesterol as sole carbon source but did grow on glucose. Of seven chemically distinct 'hits' from the library, two chemical classes of fragments were found to bind in the vicinity of the active site of HsaD by X-ray crystallography. The compounds also inhibited growth of M. tuberculosis on cholesterol. The most potent inhibitor of HsaD was also found to be the best inhibitor of mycobacterial growth on cholesterol-supplemented minimal medium. We propose that HsaD is a novel therapeutic target, which should be fully exploited in order to design and discover new anti-tubercular drugs. This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro-organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc.


  • Organizational Affiliation

    Faculty of Science, Engineering and Computing, Kingston University London, Kingston upon Thames, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
A, B
282Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: hsaDbphDRv3569c
EC: 3.7.1.17 (PDB Primary Data), 3.7.1.8 (PDB Primary Data)
UniProt
Find proteins for P9WNH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNH5 
Go to UniProtKB:  P9WNH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNH5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.03α = 90
b = 82.33β = 90
c = 194.25γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Database references
  • Version 2.0: 2024-05-08
    Changes: Advisory, Atomic model, Data collection, Database references