Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form)

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites

Kondo, J.Koganei, M.Maianti, J.P.Ly, V.L.Hanessian, S.

(2013) ChemMedChem 8: 733-739

  • DOI: https://doi.org/10.1002/cmdc.201200579
  • Primary Citation of Related Structures:  
    4GPW, 4GPX, 4GPY

  • PubMed Abstract: 

    Parasitic infections recognized as neglected tropical diseases are a source of concern for several regions of the world. Aminoglycosides are potent antimicrobial agents that have been extensively studied by biochemical and structural studies in prokaryotes. However, the molecular mechanism of their potential antiprotozoal activity is less well understood. In the present study, we have examined the in vitro inhibitory activities of some aminoglycosides with a 6'-hydroxy group on ring I and highlight that one of them, 6'-hydroxysisomicin, exhibits promising activity against a broad range of protozoan parasites. Furthermore, we have conducted X-ray analyses of 6'-hydroxysisomicin bound to the target ribosomal RNA A-sites in order to understand the mechanisms of both its antibacterial and antiprotozoal activities at the molecular level. The unsaturated ring I of 6'-hydroxysisomicin can directly stack on G1491, which is highly conserved in bacterial and protozoal species, through π-π interaction and fits closer to the guanidine base than the typically saturated and hydroxylated ring I of other structurally related aminoglycosides. Consequently, the compound adopts a lower energy conformation within the bacterial and protozoal A-sites and makes pseudo pairs to either A or G at position 1408. The A-site-selective binding mode strongly suggests that 6'-hydroxysisomicin is a potential lead for the design of next-generation aminoglycosides targeting a wide variety of infectious diseases.

  • Organizational Affiliation

    Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan. j.kondo@sophia.ac.jp


Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
A, B
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6HS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
C19 H36 N4 O8
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.791α = 90
b = 92.293β = 90
c = 47.492γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references