4BUL | pdb_00004bul

Novel hydroxyl tricyclics (e.g. GSK966587) as potent inhibitors of bacterial type IIA topoisomerases

• PDB DOI: https://doi.org/10.2210/pdb4BUL/pdb
• NAKB: 4BUL

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-06-20 Released: 2013-08-07 
• Deposition Author(s): Miles, T.J., Hennessy, A.J., Bax, B., Brooks, G., Brown, B.S., Brown, P., Cailleau, N., Chen, D., Dabbs, S., Davies, D.T., Esken, J.M., Giordano, I., Hoover, J.L., Huang, J., Jones, G.E., Sukmar, S.K.K., Spitzfaden, C., Markwell, R.E., Minthorn, E.A., Rittenhouse, S., Gwynn, M.N., Pearson, N.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Novel Hydroxyl Tricyclics (E.G., Gsk966587) as Potent Inhibitors of Bacterial Type Iia Topoisomerases.

Miles, T.J., Hennessy, A.J., Bax, B., Brooks, G., Brown, B.S., Brown, P., Cailleau, N., Chen, D., Dabbs, S., Davies, D.T., Esken, J.M., Giordano, I., Hoover, J.L., Huang, J., Jones, G.E., Kusalakumari Sukmar, S.K., Spitzfaden, C., Markwell, R.E., Minthorn, E.A., Rittenhouse, S., Gwynn, M.N., Pearson, N.D.

(2013) Bioorg Med Chem Lett 23: 5437

• PubMed: 23968823 
• DOI: https://doi.org/10.1016/j.bmcl.2013.07.013
• Primary Citation Related Structures: 
  4BUL


• PubMed Abstract: 
  

  During the course of our research to find novel mode of action antibacterials, we discovered a series of hydroxyl tricyclic compounds that showed good potency against Gram-positive and Gram-negative pathogens. These compounds inhibit bacterial type IIA topoisomerases. Herein we will discuss structure-activity relationships in this series and report advanced studies on compound 1 (GSK966587) which demonstrates good PK and in vivo efficacy properties. X-ray crystallographic studies were used to provide insight into the structural basis for the difference in antibacterial potency between enantiomers.

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Organizational Affiliation: 
• Diseases of the Developing World CEDD, GlaxoSmithKline, Madrid, Spain. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 181.45 kDa 
• Atom Count: 12,809 
• Modeled Residue Count: 1,425 
• Deposited Residue Count: 1,464 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A	A, B [auth C]	692	Staphylococcus aureus	Mutation(s): 1  EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P66937 (Staphylococcus aureus (strain N315)) Explore P66937  Go to UniProtKB:  P66937
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315)) Explore Q99XG5  Go to UniProtKB:  Q99XG5
UniProt Groups	Q99XG5P66937

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3'	C [auth E], E [auth G]	20	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3'	D [auth F], F [auth H]	20	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AE8	K [auth F]	(S)-4-((4-(((2,3-dihydro-[1,4]dioxino[2,3-c]pyridin-7-yl)methyl)amino)piperidin-1-yl)methyl)-3-fluoro-4-hydroxy-4H-pyrrolo[3,2,1-de][1,5]naphthyridin-7(5H)-one C24 H26 F N5 O4 VJVBZXRLYHVXIQ-DEOSSOPVSA-N
MN	G [auth A], H [auth A], I [auth C], J [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.871	α = 90
b = 93.871	β = 90
c = 416.439	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Miles, T.J., Hennessy, A.J., Bax, B., Brooks, G., Brown, B.S., Brown, P., Cailleau, N., Chen, D., Dabbs, S., Davies, D.T., Esken, J.M., Giordano, I., Hoover, J.L., Huang, J., Jones, G.E., Sukmar, S.K.K., Spitzfaden, C., Markwell, R.E., Minthorn, E.A., Rittenhouse, S., Gwynn, M.N., Pearson, N.D.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2013-09-18
  Changes: Database references
• Version 1.3: 2017-03-15
  Changes: Source and taxonomy
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description