Back to Table of Contents
*SYNONYM is used to test for a compound name synonym.
Four search keywords are available for chemical name searching :
You should always use *NAME or *XNAME.
The chemical name used by the author is recorded in the CSD, provided that it is "reasonable". Otherwise a systematic name is provided, wherever possible.
In a few rare cases names of the type 'Lycopodium alkaloid' or 'Compound derived by condensation of X and Y' may be the sole identification.
Two fields are available for chemical names - compound name and compound name synonym.
Only about 7% of the CSD entries have compound name synonyms and these tend to be for drug molecules.
However it should be noted that there is no strict convention regarding which name is entered in the compound name field and which in the compound name synonym field.
Since chemical name searching is a text search it is important that you are aware of certain conventions used in the CSD :
oxidation numbers of elements are recorded in lower-case Roman numerals, for example, cobalt(ii)
Greek letters are spelt in full and upper-case Greek letters are prefixed by c,
characters which would normally be typeset as superscripts or subscripts are, with the exception of some very old entries, enclosed within the characters $ (up) and ! (down) eg.: vitamin B!12$ for vitamin B12
the +/- symbol is replaced by +-
normally the elements Al,Cs,S are spelt as aluminium, cesium, sulfur
Special provisions have been made for searching for two classes of compounds:
(a) Amino-acids and Peptides
For amino-acids and peptides with basic class 48 the sequence of amino-acids is recorded in the SYNONYM field using 3-letter code symbols.
Details of how to search these sequences are discussed under *PEPTIDE and PEPTIDE-SEQ in Chapter 10.
At present the database contains over 100 bibliographic entries corresponding to published structures of oligonucleotides. Important details of these studies are recorded in the QUALIFIER field, including an indication, where appropriate, that the atomic coordinates are available from the CCDC. Until now these coordinates have not been incorporated in the database but are maintained separately.
The compound names of oligonucleotides are structured to assist searching. For example, a hexamer might be:
Oligo-6-mer d(C-G-A-T-C-G) plus daunomycin 57-hydrate.
In the COMPOUND field the name always starts with Oligo-n-mer where n indicates the number of residues.
Then follows the sequence, name of any complexed drug and an indication of the solvent content.
Graphics QUEST3D Procedure
Select *COMPOUND from the TEXT sub-menu and respond to the standard text prompts.
Basic QUEST Procedure
Ex.1 Find nickel acetylacetonate.
This compound name might be present in the CSD in a variety of forms :
Nickel acetylacetonate Nickel(ii) acetylacetonate
bis(Acetylacetonato) nickel(ii) bis(Pentane-2,4-dionato) nickel(ii)
T1 *NAME NICKEL T2 *NAME ACETYLACETON T3 *NAME PENTANE-2,4-DIONAT QUES (T3.OR.T2) .AND. T1
Ex.2 Suppose we wish to find all chemical names containing the text string PREGNEN
In this example we will illustrate the use of *XNAM.
*XNAM automatically concatenates the compound name and compound name synonym fields, compresses this text by removing blank and non-alphabetic characters, and searches the resultant text.
T1 *XNAM PREGNEN
This will register hits for names such as :
(a) 4-pregnene..................... (b) pregn-4-en-20-yne.............. (c) pregn-5(10)-en.................If we had used *NAME rather than *XNAME then hits would have been registered for (a) but not for (b) or (c).
Ex.3 Suppose you wish to find all oligonucleotide octamers
T1 *BCLA .EQ. 47 T2 *COMP OLIGO-8-MER QUES T1 .and. T2
Related Bit Screens
Relevant database bit screens are
68: oligonucleotide sequence present.
This will register hits for all oligonucleotide entries.
When the search test involves chemical names QUEST automatically generates query screens by analysing the letter-pairs in the name.
eg. PREGNEN contains the letter-pairs PR RE EG GN NE EN yielding query screens 192 169 205 202 189 212
When combining two or more chemical name tests the longer should be tested first since the query screens become more powerful as the length of the text increases.
*NAME, *PEPTIDE, *SYNONYM, *XNAME
Back to Table of Contents
Volume 2 Chapter 11 Text Menu *TEXT.