6TCK | pdb_00006tck

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with ULD-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.200 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Rational design of balanced dual-targeting antibiotics with limited resistance.

Nyerges, A.Tomasic, T.Durcik, M.Revesz, T.Szili, P.Draskovits, G.Bogar, F.Skok, Z.Zidar, N.Ilas, J.Zega, A.Kikelj, D.Daruka, L.Kintses, B.Vasarhelyi, B.Foldesi, I.Kata, D.Welin, M.Kimbung, R.Focht, D.Masic, L.P.Pal, C.

(2020) PLoS Biol 18: e3000819-e3000819

  • DOI: https://doi.org/10.1371/journal.pbio.3000819
  • Primary Citation Related Structures: 
    6TCK

  • PubMed Abstract: 

    Antibiotics that inhibit multiple bacterial targets offer a promising therapeutic strategy against resistance evolution, but developing such antibiotics is challenging. Here we demonstrate that a rational design of balanced multitargeting antibiotics is feasible by using a medicinal chemistry workflow. The resultant lead compounds, ULD1 and ULD2, belonging to a novel chemical class, almost equipotently inhibit bacterial DNA gyrase and topoisomerase IV complexes and interact with multiple evolutionary conserved amino acids in the ATP-binding pockets of their target proteins. ULD1 and ULD2 are excellently potent against a broad range of gram-positive bacteria. Notably, the efficacy of these compounds was tested against a broad panel of multidrug-resistant Staphylococcus aureus clinical strains. Antibiotics with clinical relevance against staphylococcal infections fail to inhibit a significant fraction of these isolates, whereas both ULD1 and ULD2 inhibit all of them (minimum inhibitory concentration [MIC] ≤1 μg/mL). Resistance mutations against these compounds are rare, have limited impact on compound susceptibility, and substantially reduce bacterial growth. Based on their efficacy and lack of toxicity demonstrated in murine infection models, these compounds could translate into new therapies against multidrug-resistant bacterial infections.


  • Organizational Affiliation
    • Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary.

Macromolecule Content 

  • Total Structure Weight: 49.76 kDa 
  • Atom Count: 3,407 
  • Modeled Residue Count: 376 
  • Deposited Residue Count: 424 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA gyrase subunit B
A, B
212Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.2
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus)
Explore P0A0K8 
Go to UniProtKB:  P0A0K8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0K8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N1N
(Subject of Investigation/LOI)

Query on N1N



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-phenylmethoxy-1,3-benzothiazole-6-carboxylic acid
C21 H15 Cl2 N3 O4 S
QJJVAUMJKWWKTD-UHFFFAOYSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
O [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
L [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CA

Query on CA



Download:Ideal Coordinates CCD File
N [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
N1N BindingDB:  6TCK IC50: 16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.200 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.594α = 90
b = 55.429β = 101
c = 50.976γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0208

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Data collection
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description