7M7V | pdb_00007m7v

Crystal Structure of Mtb Pks13 Thioesterase domain in complex with Compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.269 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.223 (Depositor) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target.

Wilson, C.Ray, P.Zuccotto, F.Hernandez, J.Aggarwal, A.Mackenzie, C.Caldwell, N.Taylor, M.Huggett, M.Mathieson, M.Murugesan, D.Smith, A.Davis, S.Cocco, M.Parai, M.K.Acharya, A.Tamaki, F.Scullion, P.Epemolu, O.Riley, J.Stojanovski, L.Lopez-Roman, E.M.Torres-Gomez, P.A.Toledo, A.M.Guijarro-Lopez, L.Camino, I.Engelhart, C.A.Schnappinger, D.Massoudi, L.M.Lenaerts, A.Robertson, G.T.Walpole, C.Matthews, D.Floyd, D.Sacchettini, J.C.Read, K.D.Encinas, L.Bates, R.H.Green, S.R.Wyatt, P.G.

(2022) J Med Chem 65: 409-423

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01586
  • Primary Citation Related Structures: 
    7M7V

  • PubMed Abstract: 

    With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran 1 was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against Mycobacterium tuberculosis , its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.


  • Organizational Affiliation
    • Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.

Macromolecule Content 

  • Total Structure Weight: 64.37 kDa 
  • Atom Count: 4,191 
  • Modeled Residue Count: 539 
  • Deposited Residue Count: 572 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyketide synthase Pks13
A, B
286Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pks13Rv3800c
EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6X8D2 
Go to UniProtKB:  I6X8D2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6X8D2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z3J
(Subject of Investigation/LOI)

Query on Z3J



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
5-hydroxy-2-(4-hydroxyphenyl)-N-methyl-4-[(2-oxa-6-azaspiro[3.4]octan-6-yl)methyl]-1-benzofuran-3-carboxamide
C23 H24 N2 O5
VXMQXQJRVCOGAY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.269 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.223 (Depositor) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.97α = 90
b = 110.28β = 90
c = 57.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description