6QX2

3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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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:  
    6QX1, 6QX2

  • 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 and overall design hypothesis of one series was confirmed with a co-crystal structure with DNA gyrase ...

    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. Electronic address: robert.a.stavenger@gsk.com.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BA [auth B],
M [auth S],
S [auth b],
EA [auth s]		186Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB, SAV0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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UniProt GroupP0A0K8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit A490Staphylococcus aureusMutation(s): 0 
Gene Names: gyrA, SA0006
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BC [auth D],
O [auth U],
AA [auth m]		188Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB, SAR0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BG [auth K]187Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB, SA0005, SAUSA300_0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AH [auth J]480Staphylococcus aureusMutation(s): 0 
Gene Names: gyrA, SA0006
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BI [auth M]189Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB, SA0005, SAUSA300_0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BU [auth d]181Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB, SA0005, SAR0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BY [auth k]188Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB, SA0005, SAR0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BGA [auth u]187Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB, SA0005, SAUSA300_0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')20synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')Q [auth V],
DA [auth o]		19synthetic construct
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Entity ID: 10
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')X [auth f]17synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.64α = 90
b = 410.12β = 120.22
c = 93.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Data collection