Bovine Metabolome Database: Showing metabocard for Prostaglandin D2 (BMDB0001403)

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Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:45:27 UTC

Update Date

2020-05-20 23:10:00 UTC

BMDB ID

BMDB0001403

Secondary Accession Numbers

BMDB01403

Metabolite Identification

Common Name

Prostaglandin D2

Description

Prostaglandin D2, also known as prostaglandin D2 or Prostaglandin d2, belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid. Thus, prostaglandin D2 is considered to be an eicosanoid lipid molecule. Prostaglandin D2 exists as a solid, very hydrophobic, practically insoluble (in water), and relatively neutral molecule. Prostaglandin D2 exists in all living organisms, ranging from bacteria to humans. Prostaglandin D2 participates in a number of enzymatic reactions, within cattle. In particular, Prostaglandin D2 can be converted into prostaglandin D2 through its interaction with the enzyme prostaglandin D2 receptor. In addition, Prostaglandin D2 can be converted into prostaglandin D2; which is mediated by the enzyme prostaglandin D2 receptor. In cattle, prostaglandin D2 is involved in the metabolic pathway called the intracellular signalling through prostaglandin D2 receptor and prostaglandin D2 pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(5Z,13E)-(15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate	ChEBI
(5Z,13E,15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate	ChEBI
11-Dehydroprostaglandin F2-alpha	ChEBI
PGD2	ChEBI
(5Z,13E)-(15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dienoate	Generator
(5Z,13E)-(15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid	Generator
(5Z,13E)-(15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid	Generator
(5Z,13E)-(15S)-9Α,15-dihydroxy-11-oxoprosta-5,13-dienoate	Generator
(5Z,13E)-(15S)-9Α,15-dihydroxy-11-oxoprosta-5,13-dienoic acid	Generator
(5Z,13E,15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dienoate	Generator
(5Z,13E,15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid	Generator
(5Z,13E,15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid	Generator
(5Z,13E,15S)-9Α,15-dihydroxy-11-oxoprosta-5,13-dienoate	Generator
(5Z,13E,15S)-9Α,15-dihydroxy-11-oxoprosta-5,13-dienoic acid	Generator
11-Dehydroprostaglandin F2-a	Generator
11-Dehydroprostaglandin F2-α	Generator
(5Z,13E)-(15S)-9,15-Dihydroxy-11-oxoprosta-5,13-dienoate	HMDB
(5Z,13E)-(15S)-9,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid	HMDB
(5Z,13E)-(15S)-9-alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate	HMDB
(5Z,13E)-(15S)-9-alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid	HMDB
(5Z,13E,15S)-9-alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate	HMDB
(5Z,13E,15S)-9-alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid	HMDB
(5Z,13E,15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dien-1-Oate	HMDB
(5Z,13E,15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dien-1-Oic acid	HMDB
(5Z,9-alpha,13E,15S)-9,15-Dihydroxy-11-oxo-prosta-5,13-dien-1-Oate	HMDB
(5Z,9-alpha,13E,15S)-9,15-Dihydroxy-11-oxo-prosta-5,13-dien-1-Oic acid	HMDB
(5Z,9alpha,13E,15S)-9,15-Dihydroxy-11-oxo-prosta-5,13-dien-1-Oate	HMDB
(5Z,9alpha,13E,15S)-9,15-Dihydroxy-11-oxo-prosta-5,13-dien-1-Oic acid	HMDB
11-Dehydroprostaglandin F2alpha	HMDB
9S,15S-Dihydroxy-11-oxo-5Z,13E-prostadienoate	HMDB
9S,15S-Dihydroxy-11-oxo-5Z,13E-prostadienoic acid	HMDB
F2alpha, 11-Dehydroprostaglandin	HMDB
11 Dehydroprostaglandin F2alpha	HMDB
11 Dehydroprostaglandin F2 alpha	HMDB
D2, Prostaglandin	HMDB
F2 alpha, 11-Dehydroprostaglandin	HMDB
alpha, 11-Dehydroprostaglandin F2	HMDB
11-Dehydroprostaglandin F2 alpha	HMDB

Chemical Formula

C₂₀H₃₂O₅

Average Molecular Weight

352.4651

Monoisotopic Molecular Weight

352.224974134

IUPAC Name

(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoic acid

Traditional Name

prostaglandin D2

CAS Registry Number

41598-07-6

SMILES

[H][C@](O)(CCCCC)\C=C\[C@@]1([H])C(=O)C[C@]([H])(O)[C@]1([H])C\C=C/CCCC(O)=O

InChI Identifier

InChI=1S/C20H32O5/c1-2-3-6-9-15(21)12-13-17-16(18(22)14-19(17)23)10-7-4-5-8-11-20(24)25/h4,7,12-13,15-18,21-22H,2-3,5-6,8-11,14H2,1H3,(H,24,25)/b7-4-,13-12+/t15-,16+,17+,18-/m0/s1

InChI Key

BHMBVRSPMRCCGG-OUTUXVNYSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Prostaglandins and related compounds

Alternative Parents

Substituents

Prostaglandin skeleton
Long-chain fatty acid
Hydroxy fatty acid
Cyclopentanol
Fatty acid
Unsaturated fatty acid
Cyclic alcohol
Ketone
Cyclic ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

prostaglandins D (CHEBI:15555 )
Prostaglandins (C00696 )
Prostaglandins (LMFA03010004 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Endoplasmic reticulum
Membrane

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	56 - 57 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	3.12	ALOGPS
logP	3.23	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	4.4	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	99.44 m³·mol⁻¹	ChemAxon
Polarizability	40.78 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-005i-4920000000-0865a8f516450183b07c	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-0040-4920000000-7b37e8b3ecc2583f0fdc	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-005i-4920000000-0865a8f516450183b07c	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0040-4920000000-7b37e8b3ecc2583f0fdc	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004u-8295000000-f73b3416dd6c7bbb428b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0umi-9301550000-0fbea1d102dfc38f0246	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 20V, Negative	splash10-00yr-0494000000-005f78cb3131ac258d23	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 25V, Negative	splash10-00dr-0592000000-3541be2f7c29b70b97a4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 30V, Negative	splash10-00dr-0691000000-a08a3850e6fbf73fe539	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 35V, Negative	splash10-00dr-0690000000-395bf1624fb183650268	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 40V, Negative	splash10-0079-0980000000-a0d1eacded9a909d2d07	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 45V, Negative	splash10-000i-0960000000-982ce65a71003d3086b1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 50V, Negative	splash10-0079-0930000000-15446e0930a7e4e23eff	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 55V, Negative	splash10-00di-0920000000-5f7db7776dd0364029d7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 60V, Negative	splash10-00dj-0900000000-16cfbecd58e5a59ab631	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-00yr-0494000000-65af63dd6c30ad10793d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-00dr-0592000000-3541be2f7c29b70b97a4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-00dr-0691000000-a08a3850e6fbf73fe539	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-00dr-0690000000-fef454d771f83be8e0b4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-0079-0980000000-a0d1eacded9a909d2d07	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-000i-0960000000-982ce65a71003d3086b1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-0079-0930000000-15446e0930a7e4e23eff	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-00di-0920000000-5f7db7776dd0364029d7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QIT , negative	splash10-00dj-0900000000-88efef42e905aa15039f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-00y0-0493000000-654476042b0ee0709ced	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-0019000000-c056c1df1ae03ef020cd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014r-2196000000-38a7e3f085222b728c06	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06du-9310000000-70af19409d627a582c45	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0019000000-81ee6b3c0a320262466f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0kar-2159000000-9a9fde23b29db29913b9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9520000000-d51eb51b9db8ff82e0d6	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, 100%_DMSO, experimental)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, 100%_DMSO, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Endoplasmic reticulum
Membrane

Biospecimen Locations

Adipose Tissue
Brain
Epidermis
Leukocyte
Liver
Neuron
Platelet
Smooth Muscle
Spleen

Pathways

Name	SMPDB/Pathwhiz	KEGG
Arachidonic Acid Metabolism		Not Available
Intracellular Signalling Through PGD2 receptor and Prostaglandin D2		Not Available
Fc Epsilon Receptor I Signaling in Mast Cells		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Adipose Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Brain	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Leukocyte	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Smooth Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0001403

DrugBank ID

DB02056

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022602

KNApSAcK ID

Not Available

Chemspider ID

395250

KEGG Compound ID

C00696

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

15555

References

Synthesis Reference

Ogawa, Yuji; Nunomoto, Makoto; Shibasaki, Masakatsu. A novel synthesis of prostaglandin D2. Journal of Organic Chemistry (1986), 51(9), 1625-7.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Prostaglandin-H2 D-isomerase

General function:: Involved in prostaglandin-D synthase activity
Specific function:: Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophobic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system (By similarity).
Gene Name:: PTGDS
Uniprot ID:: O02853
Molecular weight:: 21229.0

Reactions

Prostaglandin H2 → Prostaglandin D2	details

Enzyme Details

2. Prostaglandin D2 receptor

General function:: Involved in G-protein coupled receptor protein signalin
Specific function:: Receptor for prostaglandin D2 (PGD2). The activity of this receptor is mainly mediated by G(s) proteins that stimulate adenylate cyclase, resulting in an elevation of intracellular cAMP. A mobilization of calcium is also observed, but without formation of inositol 1,4,5-trisphosphate (By similarity).
Gene Name:: PTGDR
Uniprot ID:: A5D7K8
Molecular weight:: 40372.0

Showing metabocard for Prostaglandin D2 (BMDB0001403)

Structure for BMDB0001403 (Prostaglandin D2)

Enzymes

Reactions