5NQ5

Mtb TMK crystal structure in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure Guided Lead Generation toward Nonchiral M. tuberculosis Thymidylate Kinase Inhibitors.

Song, L.Merceron, R.Gracia, B.Quintana, A.L.Risseeuw, M.D.P.Hulpia, F.Cos, P.Ainsa, J.A.Munier-Lehmann, H.Savvides, S.N.Van Calenbergh, S.

(2018) J. Med. Chem. 61: 2753-2775

  • DOI: 10.1021/acs.jmedchem.7b01570
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In recent years, thymidylate kinase (TMPK), an enzyme indispensable for bacterial DNA biosynthesis, has been pursued for the development of new antibacterial agents including against Mycobacterium tuberculosis, the causative agent for the widespread ...

    In recent years, thymidylate kinase (TMPK), an enzyme indispensable for bacterial DNA biosynthesis, has been pursued for the development of new antibacterial agents including against Mycobacterium tuberculosis, the causative agent for the widespread infectious disease tuberculosis (TB). In response to a growing need for more effective anti-TB drugs, we have built upon our previous efforts toward the exploration of novel and potent Mycobacterium tuberculosis TMPK ( MtTMPK) inhibitors, and reported here the design of a novel series of non-nucleoside inhibitors of MtTMPK. The inhibitors display hitherto unexplored interactions in the active site of MtTMPK, offering new insights into structure-activity relationships. To investigate the discrepancy between enzyme inhibitory activity and the whole-cell activity, experiments with efflux pump inhibitors and efflux pump knockout mutants were performed. The minimum inhibitory concentrations of particular inhibitors increased significantly when determined for the efflux pump mmr knockout mutant, which partly explains the observed dissonance.


    Organizational Affiliation

    Laboratory for Medicinal Chemistry (FFW) , Ghent University , Ottergemsesteenweg 460 , B-9000 Gent , Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate kinase
A
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
952
Query on 952

Download SDF File 
Download CCD File 
A
5-methyl-1-[(3~{S})-1-[(3-phenoxyphenyl)methyl]piperidin-3-yl]pyrimidine-2,4-dione
C23 H25 N3 O3
UVSXXFBEAJISCP-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.390α = 90.00
b = 71.390β = 90.00
c = 133.750γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references