In a previous post ( CrystalEye links in Chemspider) and links I discussed the information and meta-information in Chemspider relating to an entry in CrystalEye. I took the first one in the collection. [I skip the second as I believe the crystallographer providing the entry for CE has misreported either the stereochemistry or the name]. I shall take the third , which links to this page. I shall here only discuss the identity of this compound.
On the CrystalEye site it is reported as a 2007 paper with the titleL-Asparagine
and the structure given refers to the conventional use of L- in aminoacids. There is no conventional structure diagram and there is no Flack parameter (which is definitive for absolute stereochemistry) – however I am assuming it is correct. As a result we computed the InChI and SMILES as:
InChI: |
InChI=1/C4H8N2O3/c5- 2(4(8)9)1- 3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2- /m0/s1 |
SMILES: |
[H]N([H]) C(=O) C([H]) ([H]) [C@]([H]) ([N+]([H]) ([H]) [H]) C(=O) [O-] |
The last part of the InChI denotes the stereochemistry and the “@” in SMILES does the same. Checking the SMILES in the Daylight Depict facility gives:
SMILES: [H]N([H])C(=O)C([H])([H])[C@]([H])([N+]([H])([H])[H])C(=O)[O-]
which seems correct.
The Chemspider page for 231 is
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Systematic Name: | 2,4-diamino-4-oxo-butanoic acid | |||||||||||||
SMILES: | O=C(N)CC(N)C(=O)O | |||||||||||||
InChI: | InChI=1/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9) | |||||||||||||
InChIKey: | DCXYFEDJOCDNAF–UHFFFAOYAL |
Data Source | External ID(s) |
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BioCyc | ASN |
ChEBI | CHEBI:22653, CHEBI:32660, CHEBI:32661 |
ChemDB | 4734684, 5183332, 5183333, 5183334, 5186560, 5260107, 5261975, 5261976, 5261977, 5262058, … |
ChemExper Chemical Directory | HeEB@BDDzTf{XZjX@@ |
ChemIDplus | 002058584, 003130878, 007006340 |
CrystalEye | Link to Record |
DiscoveryGate | 236, 522362, 5247114, 5460875 |
DTP/NCI | 159894, 186326, 186327, 186328, 196338, 82391, 206243, 210750, 210751, 218490, … |
EINECS | N/A |
MOLI | MOLI000527 |
MTDP | NSC7891, NSC82391 |
NIST | 1032224955, 1118755274, 1759855228 |
NIST Chemistry WebBook | 2489854008, 2807261232 |
Peptides | asn |
PubChem | 236, 5247114 |
Sigma-Aldrich | 11180_FLUKA, A8256_SIGMA |
Single Depositions | Asn, asparagine |
Thomson Pharma | 00062567, 00064942, 00064943, 00469703, 01920485, 01920501 |
Names and Synonyms |
Validated by Experts, Validated by Users, Non-Validated, Removed by Users, Redirected by Users, Redirect Approved by Experts
200-735-9 [EINECS/ELINCS]
2058-58-4 [RN]
218-163-3 [EINECS/ELINCS]
2-Aminosuccinamic acid
4-04-00-03005
a-Aminosuccinamic acid
Asparamide
Aspartic Acid b-Amide
2,4-diamino-4-oxobutanoic acid
221-521-1 [EINECS/ELINCS]
2-amino-3-carbamoylpropanoic acid
3130-87-8 [RN]
7006-34-0 [RN]
70-47-3 [RN]
agedoite
alpha-aminosuccinamic acid
altheine
ASN
asparagin
asparagine [Wiki]
Asparagine (VAN)
asparagine acid
Asparagine, DL-
aspartic acid beta-amide
DL-Asparagine
DL-Asparagine monohydrate
DL-Aspartamine
DL-Aspartic acid 4-amide
Hasp
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The “3D” structure appears to show D-asparagine. The picture aove appears to have no stereochemical information. From this brief survey I have not found any compounds on CS showing stereochemical information.
It seems that Chemspider strips this stereochemical information from the InChI, SMILES and coordinates that we provide on our site. This may not matter to many Chemspider visitors but it seems that it is not easy (or impossible) to find stereochemistry. Personally I am uncomfortable with DL-asparagine pointing to a structure on our site which is clearly not racemic.
Chemspider has listed under “Names and Synonyms”:
DL-Asparagine
DL-Asparagine monohydrate
To crystallographers these are completely different substances. Indeed there is a great deal of research as to what compounds form solvates and why (often called pseudopolymorphs). There is no clear way in which Chemspider can hold polymorphs, hydrates, salts, etc
On CrystalEye every CIF data_block is treated as a distinct entry and those with different cell dimensions will be regarded as distinct polymorphs. We also hold polymorphs with different temperatures and pressures as distinct entries.
In conclusion therefore, many distinct entries in CrystalEye are mapped onto a single record in Chemspider, which therefore provides the same metadata for each. In many cases this metadata (chirality, hydration) will not be correct so users should be very careful.