6FM4

The crystal structure of S. aureus Gyrase complex with ID-130 and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens.

Magaro, G.Prati, F.Garofalo, B.Corso, G.Furlotti, G.Apicella, C.Mangano, G.D'Atanasio, N.Robinson, D.Di Giorgio, F.P.Ombrato, R.

(2019) J Med Chem 62: 7445-7472

  • DOI: 10.1021/acs.jmedchem.9b00394
  • Primary Citation of Related Structures:  
    6FM4

  • PubMed Abstract: 
  • Bacterial resistance is increasing rapidly, requiring urgent identification of new antibacterial drugs that are effective against multidrug-resistant pathogens. Novel bacterial topoisomerase inhibitors (NBTIs) provide a new strategy for investigating the well-validated DNA gyrase and topoisomerase IV targets while preventing cross-resistance issues ...

    Bacterial resistance is increasing rapidly, requiring urgent identification of new antibacterial drugs that are effective against multidrug-resistant pathogens. Novel bacterial topoisomerase inhibitors (NBTIs) provide a new strategy for investigating the well-validated DNA gyrase and topoisomerase IV targets while preventing cross-resistance issues. On this basis, starting from a virtual screening campaign and subsequent structure-based hit optimization guided by X-ray studies, a novel class of piperazine-like NBTIs with outstanding enzymatic activity against Staphylococcus aureus and Escherichia coli DNA gyrase and topoisomerase IV was identified. Notably, compounds (±)-33 , (±)-35 , and (±)-36 with potent and balanced multitarget enzymatic profiles exhibited excellent efficacy against selected Gram-positive and Gram-negative pathogens, as well as clinically relevant resistant strains. Overall, the new NBTI chemotype described herein, owing to the broad-spectrum antibacterial activity and favorable in vitro safety profile, might serve as a basis for the development of novel treatments against serious infections.


    Organizational Affiliation

    Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit AA [auth B],
B [auth D]
692Staphylococcus aureus subsp. aureus N315Mutation(s): 1 
Gene Names: gyrBSA0005gyrASA0006
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP66937Q99XG5
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')C [auth E]19synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*C)-3')D [auth F]18synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DU5 (Subject of Investigation/LOI)
Query on DU5

Download Ideal Coordinates CCD File 
H [auth E]~{N}-[3-(4-isoquinolin-1-ylpiperazin-1-yl)propyl]benzamide
C23 H26 N4 O
FJTUELRAUXXLBI-UHFFFAOYSA-N
 Ligand Interaction
5UA
Query on 5UA

Download Ideal Coordinates CCD File 
G [auth E],
J [auth F]
5'-O-CARBOXY-2'-DEOXYADENOSINE
C11 H13 N5 O5
YSFXGKUPZLTGKR-RRKCRQDMSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth B],
F [auth E],
I [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.951α = 90
b = 92.951β = 90
c = 407.03γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2019-09-04
    Changes: Data collection, Database references