5NPK

1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA

• PDB DOI:  https://doi.org/10.2210/pdb5NPK/pdb
• NAKB: 5NPK

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus subsp. aureus N315, synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): Yes 


• Deposited: 2017-04-17 Released: 2017-07-12 
• Deposition Author(s): Bax, B.D., Chan, P.F., Stavenger, R.A.
• Funding Organization(s): Innovative Medicines Initiative Joint Undertaking

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.183 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.

Chan, P.F., Germe, T., Bax, B.D., Huang, J., Thalji, R.K., Bacque, E., Checchia, A., Chen, D., Cui, H., Ding, X., Ingraham, K., McCloskey, L., Raha, K., Srikannathasan, V., Maxwell, A., Stavenger, R.A.

(2017) Proc Natl Acad Sci U S A 114: E4492-E4500

• PubMed: 28507124 
• DOI: https://doi.org/10.1073/pnas.1700721114
• Primary Citation of Related Structures:  
  5NPK, 5NPP


• PubMed Abstract: 
  

A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase-DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.

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Organizational Affiliation: 

Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426; [e-mail] [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 341.5 kDa 
• Atom Count: 26,985 
• Modelled Residue Count: 2,767 
• Deposited Residue Count: 2,848 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A	A [auth B], B [auth D], E [auth b], F [auth d]	692	Staphylococcus aureus subsp. aureus N315	Mutation(s): 1  Gene Names: gyrB, SA0005, 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
Find proteins for P66937 (Staphylococcus aureus (strain N315)) Explore P66937  Go to UniProtKB:  P66937
UniProt Groups	Q99XG5P66937

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JN	CA [auth b], JA [auth e]	~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide C20 H18 N4 O S ZNBOMXQVNVLXCZ-QGZVFWFLSA-N
94H	DA [auth b], FA [auth d], J [auth B], N [auth B], Q [auth D], W [auth b]	~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide C20 H18 N4 O S ZNBOMXQVNVLXCZ-KRWDZBQOSA-N
SO4	AA [auth b]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	GA [auth d], HA [auth d], K [auth B], KA [auth e], L [auth B], M [auth B], P [auth D], R [auth D], S [auth D], T [auth D], X [auth b], Y [auth b], Z [auth b]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	EA [auth d], I [auth B], IA [auth d], O [auth D], V [auth b]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	BA [auth b]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.183 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.442	α = 90
b = 120.68	β = 90.05
c = 168.899	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Bax, B.D., Chan, P.F., Stavenger, R.A.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative Joint Undertaking		115583

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Advisory
• Version 1.2: 2018-10-24
  Changes: Advisory, Data collection, Derived calculations