8TRY

Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20348


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening.

Krieger, I.V.Yalamanchili, S.Dickson, P.Engelhart, C.A.Zimmerman, M.D.Wood, J.Clary, E.Nguyen, J.Thornton, N.Centrella, P.A.Chan, B.Cuozzo, J.W.Gengenbacher, M.Guie, M.A.Guilinger, J.P.Bienstock, C.Hartl, H.Hupp, C.D.Jetson, R.Satoh, T.Yeoman, J.T.S.Zhang, Y.Dartois, V.Schnappinger, D.Keefe, A.D.Sacchettini, J.C.

(2024) ACS Infect Dis 10: 1561-1575

  • DOI: https://doi.org/10.1021/acsinfecdis.3c00592
  • Primary Citation of Related Structures:  
    8TQG, 8TQV, 8TR4, 8TRY

  • PubMed Abstract: 

    DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.


  • Organizational Affiliation

    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.862α = 90
b = 96.623β = 90
c = 130.973γ = 90
Software Package:
Software NamePurpose
PDB-REDOrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI095208
Welch FoundationUnited StatesA-0015
Bill & Melinda Gates FoundationUnited StatesINV-040487
Department of Defense (DOD, United States)United StatesW81XWH-17-1-0692

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references