5D6P

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

• PDB DOI: https://doi.org/10.2210/pdb5D6P/pdb

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


• Deposited: 2015-08-12 Released: 2015-11-25 
• Deposition Author(s): Zhang, J., Yang, Q., Cross, J.B., Romero, J.A.C., Ryan, M.D., Lippa, B., Dolle, R.E., Andersen, O.A., Barker, J., Cheng, R.K., Kahmann, J., Felicetti, B., Wood, M., Scheich, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.257 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors.

Zhang, J., Yang, Q., Cross, J.B., Romero, J.A., Poutsiaka, K.M., Epie, F., Bevan, D., Wang, B., Zhang, Y., Chavan, A., Zhang, X., Moy, T., Daniel, A., Nguyen, K., Chamberlain, B., Carter, N., Shotwell, J., Silverman, J., Metcalf, C.A., Ryan, D., Lippa, B., Dolle, R.E.

(2015) J Med Chem 58: 8503-8512

• PubMed: 26460684 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00961
• Primary Citation of Related Structures:  
  5D6P, 5D6Q, 5D7C


• PubMed Abstract: 
  

  The emergence and spread of multidrug resistant bacteria are widely believed to endanger human health. New drug targets and lead compounds exempt from cross-resistance with existing drugs are urgently needed. We report on the discovery of azaindole ureas as a novel class of bacterial gyrase B inhibitors and detail the story of their evolution from a de novo design hit based on structure-based drug design. These inhibitors show potent minimum inhibitory concentrations against fluoroquinolone resistant MRSA and other Gram-positive bacteria.

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Organizational Affiliation: 

Cubist Pharmaceuticals Inc. , Lexington, Massachusetts 02421, United States.

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: 48.84 kDa 
• Atom Count: 3,265 
• Modelled Residue Count: 379 
• Deposited Residue Count: 424 
• Unique protein chains: 1

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
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
57U	C [auth A], F [auth B]	1-ethyl-3-[4-(hydroxymethyl)-5-(1H-pyrrol-2-yl)-1,3-thiazol-2-yl]urea C11 H14 N4 O2 S YLSYQKDIZQYYGN-UHFFFAOYSA-N
MPD	D [auth A], G [auth B], H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
57U	Binding MOAD:  5D6P	IC50: 2500 (nM) from 1 assay(s)
	BindingDB:  5D6P	IC50: 2500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.257 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.539	α = 90
b = 55.556	β = 99.73
c = 51.113	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: 2015-11-25 
Deposition Author(s): Zhang, J., Yang, Q., Cross, J.B., Romero, J.A.C., Ryan, M.D., Lippa, B., Dolle, R.E., Andersen, O.A., Barker, J., Cheng, R.K., Kahmann, J., Felicetti, B., Wood, M., Scheich, C.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description