I can find out if the compounds I have in a list belong to an organism or not using Keggrest.

compounds <- c("C06483", "C06484", "C06485")

# List of KEGG compounds
compounds <- c("C06483", "C06484", "C06485")

compounds2 <- sapply(compounds, 
                     FUN=function(x) keggrest(paste("compound", x, sep=":"),
                                              "image"))
compounds2

# Find out if the compounds belong to an organism or not
for (i in compounds) {
  if (compounds2[[i]]=="http://rest.kegg.jp/biocyc/image/compound/C06483") {
    print("this is not an organism")
  } else if (compounds2[[i]]=="http://rest.kegg.jp/biocyc/image/compound/C06484") {
    print("This is an organism")
  } else {
    print("This is not an organism")
  }
}