5CPH

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB.

Mesleh, M.F.Cross, J.B.Zhang, J.Kahmann, J.Andersen, O.A.Barker, J.Cheng, R.K.Felicetti, B.Wood, M.Hadfield, A.T.Scheich, C.Moy, T.I.Yang, Q.Shotwell, J.Nguyen, K.Lippa, B.Dolle, R.Ryan, M.D.

(2016) Bioorg.Med.Chem.Lett. 26: 1314-1318

  • DOI: 10.1016/j.bmcl.2016.01.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibitors of the ATPase function of bacterial DNA gyrase, located in the GyrB subunit and its related ParE subunit in topoisomerase IV, have demonstrated antibacterial activity. In this study we describe an NMR fragment-based screening effort target ...

    Inhibitors of the ATPase function of bacterial DNA gyrase, located in the GyrB subunit and its related ParE subunit in topoisomerase IV, have demonstrated antibacterial activity. In this study we describe an NMR fragment-based screening effort targeting Staphylococcus aureus GyrB that identified several attractive and novel starting points with good ligand efficiency. Fragment hits were further characterized using NMR binding studies against full-length S. aureus GyrB and Escherichia coli ParE. X-ray co-crystal structures of select fragment hits confirmed binding and suggested a path for medicinal chemistry optimization. The identification, characterization, and elaboration of one of these fragment series to a 0.265 μM inhibitor is described herein.


    Organizational Affiliation

    Cubist Pharmaceuticals, 65 Hayden Ave., Lexington, MA 02421, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A, B
212Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P0A0K8 (Staphylococcus aureus)
Go to UniProtKB:  P0A0K8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EVO
Query on EVO

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Download CCD File 
A, B
(3E)-3-(pyridin-3-ylmethylidene)-1,3-dihydro-2H-indol-2-one
C14 H10 N2 O
ALVGMCFQOGIUFY-XYOKQWHBSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.852α = 90.00
b = 55.681β = 100.69
c = 51.569γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Structure summary