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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    6QX2, 6QX1

  • 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: gyrBSAV0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit A490Staphylococcus aureusMutation(s): 0 
Gene Names: gyrASA0006
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
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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: gyrBSAR0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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: gyrBSA0005SAUSA300_0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AH [auth J]480Staphylococcus aureusMutation(s): 0 
Gene Names: gyrASA0006
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: gyrBSA0005SAUSA300_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: gyrBSA0005SAR0005
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: gyrBSA0005SAR0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (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: gyrBSA0005SAUSA300_0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus)
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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
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        JK8
        Query on JK8

        Download Ideal Coordinates CCD File 
        KA [auth A] , LA [auth C] , MA [auth J] , NA [auth L] , OA [auth R] , PA [auth U] , QA [auth b] , RA [auth d] , 
        KA [auth A],  LA [auth C],  MA [auth J],  NA [auth L],  OA [auth R],  PA [auth U],  QA [auth b],  RA [auth d],  SA [auth k],  TA [auth l],  UA [auth s],  VA [auth t]
        (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: 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

        View Full Validation Report



        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