6YD9

Ecoli GyrB24 with inhibitor 16a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report



Literature

Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors.

Skok, Z.Barancokova, M.Benek, O.Cruz, C.D.Tammela, P.Tomasic, T.Zidar, N.Masic, L.P.Zega, A.Stevenson, C.E.M.Mundy, J.E.A.Lawson, D.M.Maxwell, A.Kikelj, D.Ilas, J.

(2020) ACS Med Chem Lett 11: 2433-2440

  • DOI: 10.1021/acsmedchemlett.0c00416
  • Primary Citation of Related Structures:  
    6YD9

  • PubMed Abstract: 
  • We designed and synthesized a series of inhibitors of the bacterial enzymes DNA gyrase and DNA topoisomerase IV, based on our recently published benzothiazole-based inhibitor bearing an oxalyl moiety. To improve the antibacterial activity and retain pote ...

    We designed and synthesized a series of inhibitors of the bacterial enzymes DNA gyrase and DNA topoisomerase IV, based on our recently published benzothiazole-based inhibitor bearing an oxalyl moiety. To improve the antibacterial activity and retain potent enzymatic activity, we systematically explored the chemical space. Several strategies of modification were followed: varying substituents on the pyrrole carboxamide moiety, alteration of the central scaffold, including variation of substitution position and, most importantly, modification of the oxalyl moiety. Compounds with acidic, basic, and neutral properties were synthesized. To understand the mechanism of action and binding mode, we have obtained a crystal structure of compound 16a , bearing a primary amino group, in complex with the N-terminal domain of E. coli gyrase B (24 kDa) (PDB: 6YD9 ). Compound 15a , with a low molecular weight of 383 Da, potent inhibitory activity on E. coli gyrase (IC 50 = 9.5 nM), potent antibacterial activity on E. faecalis (MIC = 3.13 μM), and efflux impaired E. coli strain (MIC = 0.78 μM), is an important contribution for the development of novel gyrase and topoisomerase IV inhibitors in Gram-negative bacteria.


    Organizational Affiliation

    University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B A220Escherichia coliMutation(s): 0 
Gene Names: gyrBAW059_18890D9G42_16120
EC: 5.6.2.2
Find proteins for A0A1Y2XMI3 (Escherichia coli)
Explore A0A1Y2XMI3 
Go to UniProtKB:  A0A1Y2XMI3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ON2
Query on ON2

Download Ideal Coordinates CCD File 
A
~{N}-[6-(3-azanylpropanoylamino)-1,3-benzothiazol-2-yl]-3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrole-2-carboxamide
C16 H15 Cl2 N5 O2 S
RVKKBUSSKLNKTC-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.18α = 90
b = 67.143β = 90
c = 68.971γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)SloveniaEU H2020 ITN-ETN Project INTEGRATE (Project Reference: 642620)
European Union (EU)SloveniaEU FP7 Integrated Project MAREX (Project No. FP7-KBBE-2009-3-245137)
Academy of FinlandFinlandGrant No. 277001
Slovenian Research AgencySloveniaGrant No. P1-0208
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012523/1
Wellcome TrustUnited Kingdom110072/Z/15/Z

Revision History 

  • Version 1.0: 2020-12-30
    Type: Initial release