Crystal Structure of the Apo form of Thioesterase domain of Mtb Pks13

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13.

Aggarwal, A.Parai, M.K.Shetty, N.Wallis, D.Woolhiser, L.Hastings, C.Dutta, N.K.Galaviz, S.Dhakal, R.C.Shrestha, R.Wakabayashi, S.Walpole, C.Matthews, D.Floyd, D.Scullion, P.Riley, J.Epemolu, O.Norval, S.Snavely, T.Robertson, G.T.Rubin, E.J.Ioerger, T.R.Sirgel, F.A.van der Merwe, R.van Helden, P.D.Keller, P.Bottger, E.C.Karakousis, P.C.Lenaerts, A.J.Sacchettini, J.C.

(2017) Cell 170: 249-259.e25

  • DOI: https://doi.org/10.1016/j.cell.2017.06.025
  • Primary Citation of Related Structures:  
    5V3W, 5V3X, 5V3Y, 5V3Z, 5V40, 5V41, 5V42

  • PubMed Abstract: 

    Widespread resistance to first-line TB drugs is a major problem that will likely only be resolved through the development of new drugs with novel mechanisms of action. We have used structure-guided methods to develop a lead molecule that targets the thioesterase activity of polyketide synthase Pks13, an essential enzyme that forms mycolic acids, required for the cell wall of Mycobacterium tuberculosis. Our lead, TAM16, is a benzofuran class inhibitor of Pks13 with highly potent in vitro bactericidal activity against drug-susceptible and drug-resistant clinical isolates of M. tuberculosis. In multiple mouse models of TB infection, TAM16 showed in vivo efficacy equal to the first-line TB drug isoniazid, both as a monotherapy and in combination therapy with rifampicin. TAM16 has excellent pharmacological and safety profiles, and the frequency of resistance for TAM16 is ∼100-fold lower than INH, suggesting that it can be developed as a new antitubercular aimed at the acute infection. PAPERCLIP.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyketide synthase Pks13 (Termination polyketide synthase)
A, B
286Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pksERS027654_02263
EC: 2.7.7
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2Q5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C12 H26 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.666α = 90
b = 106.913β = 90
c = 57.815γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
SCALEPACKdata scaling
PHENIXmodel building
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description