7MVS | pdb_00007mvs

DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7MVS

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA.

Lu, Y.Vibhute, S.Li, L.Okumu, A.Ratigan, S.C.Nolan, S.Papa, J.L.Mann, C.A.English, A.Chen, A.Seffernick, J.T.Koci, B.Duncan, L.R.Roth, B.Cummings, J.E.Slayden, R.A.Lindert, S.McElroy, C.A.Wozniak, D.J.Yalowich, J.Mitton-Fry, M.J.

(2021) J Med Chem 64: 15214-15249

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01250
  • Primary Citation Related Structures: 
    7MVS

  • PubMed Abstract: 

    Novel bacterial topoisomerase inhibitors (NBTIs) are among the most promising new antibiotics in preclinical/clinical development. We previously reported dioxane-linked NBTIs with potent antistaphylococcal activity and reduced hERG inhibition, a key safety liability. Herein, polarity-focused optimization enabled the delineation of clear structure-property relationships for both microsomal metabolic stability and hERG inhibition, resulting in the identification of lead compound 79 . This molecule demonstrates potent antibacterial activity against diverse Gram-positive pathogens, inhibition of both DNA gyrase and topoisomerase IV, a low frequency of resistance, a favorable in vitro cardiovascular safety profile, and in vivo efficacy in a murine model of methicillin-resistant Staphylococcus aureus infection.


  • Organizational Affiliation
    • Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States.

Macromolecule Content 

  • Total Structure Weight: 169.39 kDa 
  • Atom Count: 12,009 
  • Modeled Residue Count: 1,389 
  • Deposited Residue Count: 1,426 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit A
A, B
693Staphylococcus aureusMutation(s): 1 
Gene Names: gyrBgyrASA0006
EC: 5.6.2.2
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus)
Explore P0A0K8 
Go to UniProtKB:  P0A0K8
Find proteins for P20831 (Staphylococcus aureus)
Explore P20831 
Go to UniProtKB:  P20831
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP20831P0A0K8
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
C, D
20synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y1W
(Subject of Investigation/LOI)

Query on Y1W



Download:Ideal Coordinates CCD File
K [auth D](1S)-2-[(2r,5S)-5-{[(2,3-dihydro-1,4-benzodioxin-6-yl)methyl]amino}-1,3-dioxan-2-yl]-1-(3-fluoro-6-methoxyquinolin-4-yl)ethan-1-ol
C25 H27 F N2 O6
OWUGLCKBNARAPP-SWDVRCMSSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MN

Query on MN



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.017α = 90
b = 93.017β = 90
c = 406.663γ = 120
Software Package:
Software NamePurpose
SBC-Collectdata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description