4PLB

Crystal Structure of S.A. gyrase-AM8191 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents.

Singh, S.B.Kaelin, D.E.Wu, J.Miesel, L.Tan, C.M.Meinke, P.T.Olsen, D.Lagrutta, A.Bradley, P.Lu, J.Patel, S.Rickert, K.W.Smith, R.F.Soisson, S.Wei, C.Fukuda, H.Kishii, R.Takei, M.Fukuda, Y.

(2014) Acs Med.Chem.Lett. 5: 609-614

  • DOI: 10.1021/ml500069w

  • PubMed Abstract: 
  • Bacterial resistance is eroding the clinical utility of existing antibiotics necessitating the discovery of new agents. Bacterial type II topoisomerase is a clinically validated, highly effective, and proven drug target. This target is amenable to in ...

    Bacterial resistance is eroding the clinical utility of existing antibiotics necessitating the discovery of new agents. Bacterial type II topoisomerase is a clinically validated, highly effective, and proven drug target. This target is amenable to inhibition by diverse classes of inhibitors with alternative and distinct binding sites to quinolone antibiotics, thus enabling the development of agents that lack cross-resistance to quinolones. Described here are novel bacterial topoisomerase inhibitors (NBTIs), which are a new class of gyrase and topo IV inhibitors and consist of three distinct structural moieties. The substitution of the linker moiety led to discovery of potent broad-spectrum NBTIs with reduced off-target activity (hERG IC50 > 18 μM) and improved physical properties. AM8191 is bactericidal and selectively inhibits DNA synthesis and Staphylococcus aureus gyrase (IC50 = 1.02 μM) and topo IV (IC50 = 10.4 μM). AM8191 showed parenteral and oral efficacy (ED50) at less than 2.5 mg/kg doses in a S. aureus murine infection model. A cocrystal structure of AM8191 bound to S. aureus DNA-gyrase showed binding interactions similar to that reported for GSK299423, displaying a key contact of Asp83 with the basic amine at position-7 of the linker.


    Organizational Affiliation

    Merck Research Laboratories , Kenilworth, New Jersey 07033, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chimera protein of DNA gyrase subunits B and A
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: 1
MoleculeChainsLengthOrganism
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')E,F20synthetic construct
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
31N
Query on 31N

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Download CCD File 
F
6-[({(1r,4S)-1-[(1S)-2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)-1-hydroxyethyl]-2-oxabicyclo[2.2.2]oct-4-yl}amino)methyl]-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one
C26 H28 F N5 O5
JWCUKLIKGBNEKA-XZZVZQAVSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.310α = 90.00
b = 93.310β = 90.00
c = 410.197γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Data collection