5D7R | pdb_00005d7r

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

• PDB DOI: https://doi.org/10.2210/pdb5D7R/pdb

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


• Deposited: 2015-08-14 Released: 2015-11-18 
• 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: 1.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Discovery of Indazole Derivatives as a Novel Class of Bacterial Gyrase B Inhibitors.

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

(2015) ACS Med Chem Lett 6: 1080-1085

• PubMed: 26487916 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00266
• Primary Citation of Related Structures:  
  5D7D, 5D7R


• PubMed Abstract: 
  

  Antibacterials with a novel mechanism of action offer a great opportunity to combat widespread antimicrobial resistance. Bacterial DNA Gyrase is a clinically validated target. Through physiochemical property optimization of a pyrazolopyridone hit, a novel class of GyrB inhibitors were discovered. Guided by structure-based drug design, indazole derivatives with excellent enzymatic and antibacterial activity as well as great animal efficacy were discovered.

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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: 49.04 kDa 
• Atom Count: 3,613 
• Modelled Residue Count: 380 
• 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 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus) Explore P0A0K8  Go to UniProtKB:  P0A0K8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
57Y	H [auth A], O [auth B]	3-hydroxy-5-[5-(6-hydroxy-7-propyl-2H-indazol-3-yl)-1,3-thiazol-2-yl]pyridine-2-carboxylic acid C19 H16 N4 O4 S YZWBQSFGTLQFTB-UHFFFAOYSA-N
MPD	M [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	G [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.192	α = 90
b = 55.514	β = 100.65
c = 51.114	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
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: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description