5IWI | pdb_00005iwi

1.98A structure of GSK945237 with S.aureus DNA gyrase and singly nicked DNA

• PDB DOI: https://doi.org/10.2210/pdb5IWI/pdb
• NAKB: 5IWI

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus, Staphylococcus aureus subsp. aureus N315, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-22 Released: 2016-05-25 
• Deposition Author(s): Bax, B.D., Miles, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Novel tricyclics (e.g., GSK945237) 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., Jones, G.E., Kusalakumari Sukmar, S.K., Markwell, R.E., Minthorn, E.A., Rittenhouse, S., Gwynn, M.N., Pearson, N.D.

(2016) Bioorg Med Chem Lett 26: 2464-2469

• PubMed: 27055939 
• DOI: https://doi.org/10.1016/j.bmcl.2016.03.106
• Primary Citation Related Structures: 
  5IWI, 5IWM


• PubMed Abstract: 
  

  During the course of our research on the lead optimisation of the NBTI (Novel Bacterial Type II Topoisomerase Inhibitors) class of antibacterials, we discovered a series of tricyclic compounds that showed good Gram-positive and Gram-negative potency. Herein we will discuss the various subunits that were investigated in this series and report advanced studies on compound 1 (GSK945237) which demonstrates good PK and in vivo efficacy properties.

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Organizational Affiliation: 
• Diseases of the Developing World CEDD, GlaxoSmithKline, Calle Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain. Electronic address: [e-mail].
Infectious Diseases CEDD, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK.
Platform Technology & Science, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK.
Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK.
Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.
Diseases of the Developing World CEDD, GlaxoSmithKline, Calle Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain.
Oncology TA, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 170.05 kDa 
• Atom Count: 14,196 
• Modeled Residue Count: 1,385 
• Deposited Residue Count: 1,424 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit B	A [auth B], C [auth D]	202	Staphylococcus aureus	Mutation(s): 0  Gene Names: gyrB, SA0005 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	B [auth A], D [auth C]	490	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0  Gene Names: gyrA, SA0006 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315)) Explore Q99XG5  Go to UniProtKB:  Q99XG5

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')	E	20	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')	F	8	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')	G	12	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6EJ	V [auth E]	(1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one C24 H26 F N5 O3 SRICOHRDRMZREQ-MRXNPFEDSA-N
GOL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth C], S [auth C], T [auth C], U [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	H [auth B], P [auth D], Q [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.897	α = 90
b = 92.897	β = 90
c = 410.784	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Bax, B.D., Miles, T.J.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description