Biomedical Engineering Reference
In-Depth Information
defi ned
E
orientation and stereochemistry. Examining the PubChem records
gives the following list of chemical names describing the side chain showing
the distinct variation and confusion across the set of molecules labeled vitamin
K
1
in the PubChem database.
• 2 - Methyl - 3 - [(
E
,7
R
,11
R
) - 3,7,11,15 - tetramethyl -
• 2 - Methyl - 3 - [(
E
,7
S
,11
R
) - 3,7,11,15 - tetramethyl -
• 2 - Methyl - 3 - [(
E
,7
R
,11
S
) - 3,7,11,15 - tetramethyl -
• 2 - Methyl - 3 - [(
E
,7
S
,11
S
) - 3,7,11,15 - tetramethyl -
• 2 - Methyl - 3 - [(
E
,11
S
) - 3,7,11,15 - tetramethyl -
• 2 - Methyl - 3 - [(
E
) - 3,7,11,15 - tetramethyl -
• 2 - Methyl - 3 - (3,7,11,15 - tetramethyl -
• 2 - Methyl - 3 - [(
E
) - 3,7,11,15 - tetramethyl -
Attempting to declare the correct structure for vitamin K
1
from the data
extracted from this series of public domain databases is clearly challenging.
Two of the most highly respected and curated collections of structure-based
data are the Merck Index [49] and the CAS Registry [50] from the Chemical
Abstracts Service (CAS). CAS has made a subset of its tens of millions of
structures available online as the Common Chemistry [51] public collection
and fortunately vitamin K
1
is available in the database [52] as well as in the
Merck Index. Figure 22.1 shows the structures from both sources, and they are
consistent with an
E
orientation and
R
,
R
stereochemistry in the side chain. Of
the public domain databases listed, only ChEBI [53] and ChemSpider [54] are
consistent with the Common Chemistry and Merck Index structures. We will
assert
from these data that vitamin K
1
is the structure listed in ChEBI,
ChemSpider, Common Chemistry, and the Merck Index. The errors found in
Wikipedia, PubChem, KEGG, and DrugBank are representative of the quality
of data online. This situation has been further exemplifi ed in searches for the
chemical structures of Taxol [55], vancomycin [56], and domoic acid [57]. While
the structures of each of these compounds have now been ascertained and
validated on ChemSpider, the structure of digitonin remains an issue and com-
munity involvement has failed to assert the structure as yet [58]. Public com-
pound databases on the Internet are mixed quality and, in all cases, require
ongoing validation. The reader should at all times use caution and not take
the structures at face value from the Web. The validation of assertion-based
data such as chemical names and identifi ers contained within a chemical data-
base is challenging enough. The validation of experimentally determined
data for millions of compounds is essentially an impossible task without
remeasurement.
With an intention to provide a trusted resource there was a clear and
obvious need for data curation and validation of the data imported to
ChemSpider. Since the ChemSpider team was both small and voluntary, there
was no easy manner by which to perform data validation without engaging the
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