5BS3

Crystal Structure of S.A. gyrase in complex with Compound 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2).

Singh, S.B.Kaelin, D.E.Wu, J.Miesel, L.Tan, C.M.Black, T.Nargund, R.Meinke, P.T.Olsen, D.B.Lagrutta, A.Lu, J.Patel, S.Rickert, K.W.Smith, R.F.Soisson, S.Sherer, E.Joyce, L.A.Wei, C.Peng, X.Wang, X.Fukuda, H.Kishii, R.Takei, M.Takano, H.Shibasaki, M.Yajima, M.Nishimura, A.Shibata, T.Fukuda, Y.

(2015) Bioorg.Med.Chem.Lett. 25: 1831-1835

  • DOI: 10.1016/j.bmcl.2015.03.044

  • PubMed Abstract: 
  • Novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of broad-spectrum antibacterial agents targeting bacterial Gyrase A and ParC and have potential utility in combating antibiotic resistance. A series of novel oxabicyclooctane-link ...

    Novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of broad-spectrum antibacterial agents targeting bacterial Gyrase A and ParC and have potential utility in combating antibiotic resistance. A series of novel oxabicyclooctane-linked NBTIs with new tricyclic-1,5-naphthyridinone left hand side moieties have been described. Compounds with a (R)-hydroxy-1,5-naphthyridinone moiety (7) showed potent antibacterial activity (e.g., Staphylococcus aureus MIC 0.25 μg/mL), acceptable Gram-positive and Gram-negative spectrum with rapidly bactericidal activity. The compound 7 showed intravenous and oral efficacy (ED50) at 3.2 and 27 mg/kg doses, respectively, in a murine model of bacteremia. Most importantly they showed significant attenuation of functional hERG activity (IC50 >170 μM). In general, lower logD attenuated hERG activity but also reduced Gram-negative activity. The co-crystal structure of a hydroxy-tricyclic NBTI bound to a DNA-gyrase complex exhibited a binding mode that show enantiomeric preference for R isomer and explains the activity and SAR. The discovery, synthesis, SAR and X-ray crystal structure of the left-hand-side tricyclic 1,5-naphthyridinone based oxabicyclooctane linked NBTIs are described.


    Organizational Affiliation

    Merck Research Laboratories, Kenilworth, NJ 07033, United States. Electronic address: sheo.singh.215@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A and B
B, D
692Staphylococcus aureusMutation(s): 2 
Gene Names: gyrB, gyrA
EC: 5.6.2.3 5.6.2.3
Find proteins for P0A0K8 (Staphylococcus aureus)
Go to UniProtKB:  P0A0K8
Find proteins for P20831 (Staphylococcus aureus)
Go to UniProtKB:  P20831
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(P*AP*GP*CP*CP*G)-D(P*T)-R(P*AP*GP*GP*GP*CP*CP*C)-D(P*T)-R(P*AP*CP*GP*GP*C)-D(P*T)-3')E,F20Staphylococcus aureus subsp. aureus ED98
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
B, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
WCP
Query on WCP

Download SDF File 
Download CCD File 
F
(4R)-3-fluoro-4-hydroxy-4-{[(1r,4R)-4-{[(3-oxo-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-6-yl)methyl]amino}-2-oxabicyclo[2.2.2]oct-1-yl]methyl}-4,5-dihydro-7H-pyrrolo[3,2,1-de][1,5]naphthyridin-7-one
C26 H26 F N5 O5
XTHQMKOHGLBSON-GSDHBNRESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.337α = 90.00
b = 93.337β = 90.00
c = 411.068γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
REFMACphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release