Crystallography Open Database

Information card for entry 2215294

Preview

Coordinates	2215294.cif
Structure factors	2215294.hkl
Original IUCr paper	HTML
External links	ChemSpider; PubChem

Structure parameters

Common name	(2<i>S</i>,3<i>R</i>,4<i>R</i>,5<i>S</i>)-3,4,5-Trihydroxypipecolic acid dihydrate
Chemical name	(2<i>S</i>,3<i>R</i>,4<i>R</i>,5<i>S</i>)-3,4,5-Trihydroxypiperidine-2-\ carboxylic acid dihydrate
Formula	C6 H15 N O7
Calculated formula	C6 H15 N O7
SMILES	[C@H]1([C@H]([C@@H]([C@H](CN1)O)O)O)C(=O)O.O.O
Title of publication	(2<i>S</i>,3<i>R</i>,4<i>R</i>,5<i>S</i>)-3,4,5-Trihydroxypipecolic acid dihydrate [(2<i>S</i>,3<i>R</i>,4<i>R</i>,5<i>S</i>)-3,4,5-trihydroxypiperidine-2-carboxylic acid dihydrate]
Authors of publication	Kathrine V. Booth; Sarah F. Jenkinson; Watkin, David J.; Hazel Sharp; Paul Wyn Jones; Robert J. Nash; George W. J. Fleet
Journal of publication	Acta Crystallographica Section E
Year of publication	2007
Journal volume	63
Journal issue	9
Pages of publication	o3783 - o3784
a	6.4536 ± 0.0002 Å
b	6.7954 ± 0.0002 Å
c	20.7965 ± 0.0008 Å
α	90°
β	90°
γ	90°
Cell volume	912.03 ± 0.05 Å³
Cell temperature	150 K
Ambient diffraction temperature	150 K
Number of distinct elements	4
Space group number	19
Hermann-Mauguin space group symbol	P 21 21 21
Hall space group symbol	P 2ac 2ab
Residual factor for all reflections	0.0417
Residual factor for significantly intense reflections	0.0381
Weighted residual factors for all reflections	0.0973
Weighted residual factors for significantly intense reflections	0.0954
Weighted residual factors for all reflections included in the refinement	0.0973
Goodness-of-fit parameter for all reflections included in the refinement	0.9684
Diffraction radiation wavelength	0.71073 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	Yes

Version history

Revision	Date	Message	Files
301804 (current)	2025-08-19	Add cross-references to PubChem compounds in COD range 2/21 Each referenced PubChem compound corresponds to the full crystal structure.	2215294.cif 2215294.hkl
201974	2017-10-13	cif/2/ Marking COD entries in range 2/21 that are known to be related to ChemSpider entries using the _cod_related_entry data loop.	2215294.cif 2215294.hkl
181072	2016-04-03	hkl/2/21/ (antanas@echidna) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in subrange 2/21/52.	2215294.cif 2215294.hkl
176432	2016-02-14	cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries.	2215294.cif 2215294.hkl
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2215294.cif 2215294.hkl
88064	2013-08-29	Adding _cod_database_fobs_code data item to all COD CIFs that have Fobs deposited and did not have this data item yet.	2215294.cif 2215294.hkl
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2215294.cif 2215294.hkl
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2215294.cif 2215294.hkl
26029	2011-09-17	cif/2/ Reverting changes of revision 25271: ( cd cif/2/; svn merge -r25271:25270 . ) The problem was that the reprocessed files from IUCr, although were more complete, "resurrected" data errors that were corrected in the previous recisions. The additional data that have been extracted during the reprocessing will have to be merged without overwriting the existing values in COD files, except some explicit and controlled cases (such as publication titles and chemical names).	2215294.cif 2215294.hkl
26025	2011-09-16	hkl/2/ Adding assigned Fobs files for the 1980-2010 IUCr data.	2215294.cif 2215294.hkl
25271	2011-09-10	cif/2/ Adding reporocessed IUCr CIFs for the years 1980-2010. The CIFs now contain more complete bibliography, substance names, correctly unfolded text fields (using the CIF line unfolding protocol), explicitely set cell angles, and _cod_data_source_block fields.	2215294.cif
5310	2011-01-02	cif/ Running cif_fix_enum with the core CIF dictionary on COD ranges 2, 8 and 9. Range 9 remained unchanged, and in ranges 2 and 8 there were 17309 modified files, most changes were fixes enumerator case.	2215294.cif
966	2010-01-30	cif/ Adding _cod_database_code tags to all COD entries. Adding tag description to the cif_cod.dic dictionary so that COD entries can be validated.	2215294.cif
858	2009-11-18	cod/cif/ Changing all _chemical_formula_sum values, were necessary, to conform IUCr recommended syntax and sorting order. After this operation, it will be easier to search for structures using the _chemical_formula_sum values. Only those files and thos lines that really needed to be changed were changed; otehrwise the CIFs were not reformatted. The procedure was as follows: first, all files were passed through a 'cif_filter --parse-formula-sum' command, and the lines containing _cif_formula_sum matching tags were extracted. The extracted tags were "spliced" into the CIF files using the ./bin/{un,}grepciftag commands and awk to filter out old tags and add new tags in their place; the replacement was only done if the new tags contained "_cod_" tags ('grep -q _cod_ tmp-$$'), indicating that cif_filter has altered the formula, or the original file did not contain the _chemical_formula_sum tag ('! grep -q _chemical_formula_sum X'), indicating that cif_filter has guessed the chemical_formula_sum from the file (which should not have happened, actually). If the file was different, disregarding spaces, from the original one ('if ! diff -wb X tmp2-$$'), the original was replaced by the new file, to be committed to the repository. The full command for this step was: ( \ set -x; \ find ? -name \.cif \ \| xargs -n1 -iX \ sh -c 'cif_filter --parse-formula-sum X \ \| ./bin/grepciftag _chemical_formula_sum > tmp-$$; \ if grep -q _cod_ tmp-$$ \|\| ! grep -q _chemical_formula_sum X; \ then \ awk "/^#/,/_chemical_formula_sum/{print} /_chemical_formula_sum/{exit}" X \ \| ./bin/ungrepciftag _chemical_formula_sum > tmp2-$$; \ cat tmp-$$ >> tmp2-$$; \ awk "/_chemical_formula_sum/,/\$eof/" X \ \| ./bin/ungrepciftag _chemical_formula_sum >> tmp2-$$; \ if ! diff -wb X tmp2-$$; \ then \ mv -fv tmp2-$$ X; \ fi; \ fi; \ rm -f tmp-$$ tmp2-$$' \ ) >& sort-chemical-formulae-2009.11.16.log Next, the files were searched that differ from their originals only by the order of CIF tags: svn st \ \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ bash -c 'if diff -q <(svn cat X\|sort) <(sort X) >& /dev/null; \ then echo X; \ fi' \ >& only-reordered.lst These files, after manual inspection ('cat only-reordered.lst \| xargs svn diff \| less'), were reverted to the originals: cat only-reordered.lst \| xargs svn revert Finally, a syntax check was performed using 'vcif': svn st \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-check-2009.11.18.err A check on the whole COD archive showed the same files as recorded in vcif-check-2009.11.18.err: find ? -name \.cif \ \| sort \ \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; \ vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-all-check-`-date`.err diff vcif-check-2009.11.18.err vcif-all-check-2009.11.18.err Since no differences were detected in between vcif-check-2009.11.18.err and vcif-all-check-2009.11.18.err, the latter was deleted and is not committed. The check reveled two broken files, 2/2000267.cif and 2/2001000.cif; these were corrected manually. Afther this, one more 'vcif' check showed no syntax errors, and the changes are committed into the COD repository. 19798 files have modifications in this commit, according to svn st \| grep '^M' \| wc -l	2215294.cif
326	2008-04-03	Adding all Acta Cryst. B, C, and E missing retrospective CIF files up to 2008 February, generated from the files that were automatically downloaded from the IUCr site.	2215294.cif