Structure Database (LMSD)

Common Name
tetranor-PGDM
Systematic Name
9S-hydroxy-11,15-dioxo-2,3,4,5-tetranor-prostan-1,20-dioic acid
Synonyms
LM ID
LMFA03010221
Formula
C16H24O7
Exact Mass
Calculate m/z
328.152205
Sum Composition
FA 16:4;O5
Status
Curated
Show lipids differing only in stereochemistry/bond geometry
View spectra on LIPID MAPS Standard Spectra DB
View studies deposited in Metabolomics Workbench in which this molecule has been identified

Classification

Category
Main Class
Sub Class
Fatty Acyls [FA]
Eicosanoids [FA03]
Prostaglandins [FA0301]
Fatty Acids and Conjugates [FA01]
Carbocyclic fatty acids [FA0114]
Hydroxy fatty acids [FA0105]
Oxo fatty acids [FA0106]

Biological Context

Prostaglandin D2 (PGD2) is synthesized by hematopoietic-type PGD-synthase (H-PGDS) in mast cells and is released in large quantities during allergic and asthmatic anaphylaxis.1 PGD2 is also produced in the brain by lipocalin-PGD-synthase also known as β-trace.2,3 In the brain, PGD2 produces normal physiological sleep and lowering of body temperature.2,3 Further pharmacological actions include inhibition of platelet aggregation and relaxation of vascular smooth muscle.4 tetranor-PGDM is a major metabolite of PGD2 that is detectable in human and mouse urine.5 The levels of tetranor-PGDM and 2,3-dinor-11β-PGF2α , a related PGD2 metabolite, in human urine were found to be 1.5 ± 0.3 and 0.6 ± ng/mg creatinine, respectively. tetranor-PGDM was detected in murine urine at a level of 8.1 ± 1.3 ng/mg creatinine.5

This information has been provided by Cayman Chemical

References

1. Hayaishi, O. Sleep-wake regulation by prostaglandins D2 and E2. The Journal of Biological Chemisty 263(29), 14593-14596 (1988).
2. Roberts, L.J., II, and Sweetman, B.J. Metabolic fate of endogenously synthesized prostaglandin D2 in a human female with mastocytosis. Prostaglandins 30(3), 383-400 (1985).
3. Giles, H., and Leff, P. The biology and pharmacology of PGD2. Prostaglandins 35(2), 277-300 (1988).
4. Onoe, H., Ueno, R., Fujita, I., et al. Prostaglandin D2, a cerebral sleep-inducing substance in monkeys. Proc. Natl. Acad. Sci. USA 85(11), 4082-4086 (1988).
5. Song, W.L., Wang, M., Ricciotti, E., et al. Tetranor PGDM, an abundant urinary metabolite reflects biosynthesis of prostaglandin D2 in mice and humans. The Journal of Biological Chemisty 283(2), 1179-1188 (2008).

References

Taxonomy Information

Curated from
NCBI taxonomy class
Reference
Homo sapiens (#9606)
Mammalia (#40674)
Tetranor PGDM, an abundant urinary metabolite reflects biosynthesis of prostaglandin D2 in mice and humans.,
J Biol Chem, 2008
Pubmed ID: 17993463

String Representations

InChiKey (Click to copy)
VNJBSPJILLFAIC-BZPMIXESSA-N
InChi (Click to copy)
InChI=1S/C16H24O7/c17-10(3-1-2-4-15(20)21)5-6-11-12(7-8-16(22)23)14(19)9-13(11)18/h11-12,14,19H,1-9H2,(H,20,21)(H,22,23)/t11-,12-,14+/m1/s1
SMILES (Click to copy)
[C@H]1(CCC(=O)CCCCC(=O)O)C(=O)C[C@H](O)[C@@H]1CCC(=O)O

Other Databases

CHEBI ID
165343
PubChem CID
44600448
Cayman ID
12850

Calculated Physicochemical Properties

Heavy Atoms 23
Rings 1
Aromatic Rings 0
Rotatable Bonds 11
Van der Waals Molecular Volume 323.97
Topological Polar Surface Area 128.97
Hydrogen Bond Donors 3
Hydrogen Bond Acceptors 7
logP 1.70
Molar Refractivity 80.34

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Created at
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Updated at
15th Nov 2024