4UNN

Mtb TMK in complex with compound 8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure Guided Lead Generation for M. Tuberculosis Thymidylate Kinase (Mtb Tmk): Discovery of 3-Cyanopyridone and 1,6-Naphthyridin-2-One as Potent Inhibitors.

Naik, M., Raichurkar, A., Bandodkar, B.S., Varun, B.V., Bhat, S., Kalkhambkar, R., Murugan, K., Menon, R., Bhat, J., Paul, B., Iyer, H., Hussein, S., Tucker, J.A., Vogtherr, M., Embrey, K.J., Mcmiken, H., Prasad, S., Gill, A., Ugarkar, B.G., Venkatraman, J., Read, J., Panda, M.

(2015) J.Med.Chem. 58: 753

  • DOI: 10.1021/jm5012947
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • M. tuberculosis thymidylate kinase (Mtb TMK) has been shown in vitro to be an essential enzyme in DNA synthesis. In order to identify novel leads for Mtb TMK, we performed a high throughput biochemical screen and an NMR based fragment screen through ...

    M. tuberculosis thymidylate kinase (Mtb TMK) has been shown in vitro to be an essential enzyme in DNA synthesis. In order to identify novel leads for Mtb TMK, we performed a high throughput biochemical screen and an NMR based fragment screen through which we discovered two novel classes of inhibitors, 3-cyanopyridones and 1,6-naphthyridin-2-ones, respectively. We describe three cyanopyridone subseries that arose during our hit to lead campaign, along with cocrystal structures of representatives with Mtb TMK. Structure aided optimization of the cyanopyridones led to single digit nanomolar inhibitors of Mtb TMK. Fragment based lead generation, augmented by crystal structures and the SAR from the cyanopyridones, enabled us to drive the potency of our 1,6-naphthyridin-2-one fragment hit from 500 μM to 200 nM while simultaneously improving the ligand efficiency. Cyanopyridone derivatives containing sulfoxides and sulfones showed cellular activity against M. tuberculosis. To the best of our knowledge, these compounds are the first reports of non-thymidine-like inhibitors of Mtb TMK.

    Organizational Affiliation: 

    Department of Chemistry, and ‡Department of Bioscience, Innovative Medicines Infection, AstraZeneca India Pvt. Ltd. , Bellary Road, Hebbal, Bangalore, Karnataka 560024, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE KINASE
A, B
214Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: tmk
EC: 2.7.4.9
Find proteins for P9WKE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WKE1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QZZ
Query on QZZ
Download SDF File 
Download CCD File 
A, B
4-[3-cyano-6-(3-methoxyphenyl)-2-oxo-1H-pyridin-4-yl]benzoic acid
C20 H14 N2 O4
DYVOFZNYRIDQOP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.135 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 75.624α = 90.00
b = 75.624β = 90.00
c = 71.140γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references