6QX1

2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.

Thalji, R.K.Raha, K.Andreotti, D.Checchia, A.Cui, H.Meneghelli, G.Profeta, R.Tonelli, F.Tommasi, S.Bakshi, T.Donovan, B.T.Howells, A.Jain, S.Nixon, C.Quinque, G.McCloskey, L.Bax, B.D.Neu, M.Chan, P.F.Stavenger, R.A.

(2019) Bioorg.Med.Chem.Lett. 29: 1407-1412

  • DOI: 10.1016/j.bmcl.2019.03.029
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of DNA gyrase inhibitors were designed based on the X-ray structure of a parent thiophene scaffold with the objective to improve biochemical and whole-cell antibacterial activity, while reducing cardiac ion channel activity. The binding mode ...

    A series of DNA gyrase inhibitors were designed based on the X-ray structure of a parent thiophene scaffold with the objective to improve biochemical and whole-cell antibacterial activity, while reducing cardiac ion channel activity. The binding mode and overall design hypothesis of one series was confirmed with a co-crystal structure with DNA gyrase. Although some analogs retained both biochemical activity and whole-cell antibacterial activity, we were unable to significantly improve the activity of the series and analogs retained activity against the cardiac ion channels, therefore we stopped optimization efforts.


    Organizational Affiliation

    GlaxoSmithKline, Collegeville, PA 19426, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
B, D
202Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, C
490Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrA
EC: 5.6.2.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')E,F20synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
B, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

Download SDF File 
Download CCD File 
C
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
JK8
Query on JK8

Download SDF File 
Download CCD File 
B, D
(2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine
C21 H17 Cl N2 O2
HHSLFPVGKCXEOG-FQEVSTJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.190α = 90.00
b = 93.190β = 90.00
c = 408.990γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-06 
  • Released Date: 2019-04-17 
  • Deposition Author(s): Bax, B.D.

Funding OrganizationLocationGrant Number
European Union115583

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references