5U94

Crystal structure of the Mycobacterium tuberculosis PASTA kinase PknB in complex with the potential theraputic kinase inhibitor GSK690693.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

In Silico Screen and Structural Analysis Identifies Bacterial Kinase Inhibitors which Act with beta-Lactams To Inhibit Mycobacterial Growth.

Wlodarchak, N.Teachout, N.Beczkiewicz, J.Procknow, R.Schaenzer, A.J.Satyshur, K.Pavelka, M.Zuercher, W.Drewry, D.Sauer, J.D.Striker, R.

(2018) Mol. Pharm. 15: 5410-5426

  • DOI: 10.1021/acs.molpharmaceut.8b00905

  • PubMed Abstract: 
  • New tools and concepts are needed to combat antimicrobial resistance. Actinomycetes and firmicutes share several eukaryotic-like Ser/Thr kinases (eSTK) that offer antibiotic development opportunities, including PknB, an essential mycobacterial eSTK. ...

    New tools and concepts are needed to combat antimicrobial resistance. Actinomycetes and firmicutes share several eukaryotic-like Ser/Thr kinases (eSTK) that offer antibiotic development opportunities, including PknB, an essential mycobacterial eSTK. Despite successful development of potent biochemical PknB inhibitors by many groups, clinically useful microbiologic activity has been elusive. Additionally, PknB kinetics are not fully described, nor are structures with specific inhibitors available to inform inhibitor design. We used computational modeling with available structural information to identify human kinase inhibitors predicted to bind PknB, and we selected hits based on drug-like characteristics intended to increase the likelihood of cell entry. The computational model suggested a family of inhibitors, the imidazopyridine aminofurazans (IPAs), bind PknB with high affinity. We performed an in-depth characterization of PknB and found that these inhibitors biochemically inhibit PknB, with potency roughly following the predicted models. A novel X-ray structure confirmed that the inhibitors bound as predicted and made favorable protein contacts with the target. These inhibitors also have antimicrobial activity toward mycobacteria and nocardia. We demonstrated that the inhibitors are uniquely potentiated by β-lactams but not antibiotics traditionally used to treat mycobacteria, consistent with PknB's role in sensing cell wall stress. This is the first demonstration in the phylum actinobacteria that some β-lactam antibiotics could be more effective if paired with a PknB inhibitor. Collectively, our data show that in silico modeling can be used as a tool to discover promising drug leads, and the inhibitors we discovered can act with clinically relevant antibiotics to restore their efficacy against bacteria with limited treatment options.


    Organizational Affiliation

    School of Medicine and Dentistry , University of Rochester Medical Center , 601 Elmwood Ave. , Rochester , New York 14620 , United States.,William S. Middleton Memorial Veterans Hospital , 2500 Overlook Terr. , Madison , Wisconsin 53705 , United States.,Department of Medicine , University of Wisconsin-Madison , 3341 Microbial Sciences Building, 1550 Linden Dr. , Madison , Wisconsin 53706 , United States.,Small Molecule Screening Facility, Carbone Cancer Center , University of Wisconsin-Madison , 1111Highland Ave. , Madison , Wisconsin 53705 , United States.,Department of Medical Microbiology and Immunology , University of Wisconsin-Madison , 4203 Microbial Sciences Building, 1550 Linden Dr. , Madison , Wisconsin 53706 , United States.,Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , SGC Center for Chemical Biology, 120 Mason Farm Rd. , Chapel Hill , North Carolina 27599 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PknB
A
285Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: pknB
EC: 2.7.11.1
Find proteins for P9WI81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WI81
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
G93
Query on G93

Download SDF File 
Download CCD File 
A
4-{2-(4-amino-1,2,5-oxadiazol-3-yl)-1-ethyl-7-[(3S)-piperidin-3-ylmethoxy]-1H-imidazo[4,5-c]pyridin-4-yl}-2-methylbut-3-yn-2-ol
GSK690693
C21 H27 N7 O3
KGPGFQWBCSZGEL-ZDUSSCGKSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 114.786α = 90.00
b = 121.294β = 90.00
c = 49.529γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Advancing Translational SciencesUnited StatesUL1TR000427
Hartwell FoundationUnited States--

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Author supporting evidence
  • Version 1.2: 2018-04-18
    Type: Data collection
  • Version 1.3: 2019-01-16
    Type: Data collection, Database references