Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.62 kDa 
• Atom Count: 3,704 
• Modelled Residue Count: 378 
• Deposited Residue Count: 424 
• Unique protein chains: 1

 5CPH

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

• PDB DOI: 10.2210/pdb5CPH/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-21 Released: 2016-02-03 
• Deposition Author(s): Andersen, O.A., Barker, J., Cheng, R.K., Kahmann, J., Felicetti, B., Wood, M., Scheich, C., Mesleh, M., Cross, J.B., Zhang, J., Yang, Q., Lippa, B., Ryan, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.194 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

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

• PubMed: 26786695 
• DOI: 10.1016/j.bmcl.2016.01.009
• Primary Citation of Related Structures:  
  5CPH, 5CTU, 5CTW, 5CTX, 5CTY


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A, B	212	Staphylococcus aureus	Mutation(s): 0  Gene Names: gyrB EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus) Explore P0A0K8  Go to UniProtKB:  P0A0K8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EVO	C [auth A], F [auth B]	(3E)-3-(pyridin-3-ylmethylidene)-1,3-dihydro-2H-indol-2-one C14 H10 N2 O ALVGMCFQOGIUFY-XYOKQWHBSA-N
MPD	E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	D [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
EVO	BindingDB:  5CPH	IC50: 8.40e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.194 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.852	α = 90
b = 55.681	β = 100.69
c = 51.569	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Andersen, O.A., Barker, J., Cheng, R.K., Kahmann, J., Felicetti, B., Wood, M., Scheich, C., Mesleh, M., Cross, J.B., Zhang, J., Yang, Q., Lippa, B., Ryan, M.D.

Revision History  

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