Livestock Metabolome Database: Showing metabocard for CDP (LMDB00346)

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-07-13 19:47:48 UTC

Update Date

2016-07-20 21:00:01 UTC

Lmdb

LMDB00346

Secondary Accession Numbers

None

Metabolite Identification

Common Name

CDP

Description

CDP, also known as 5'-CDP, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. CDP is an extremely weak basic (essentially neutral) compound (based on its pKa). CDP exists in all living species, ranging from bacteria to humans. In humans, CDP is involved in cardiolipin biosynthesis. Outside of the human body, CDP has been detected, but not quantified in, several different foods, such as carobs, mexican oregano, evergreen huckleberries, green vegetables, and pepper (c. baccatum). This could make CDP a potential biomarker for the consumption of these foods.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
5'-CDP	ChEBI
Cytidine 5'-diphosphate	ChEBI
Cytidine 5'-diphosphoric acid	ChEBI
Cytidine 5'-pyrophosphate	ChEBI
Cytidine diphosphate	ChEBI
Cytidine, 5'-(trihydrogen pyrophosphate)	ChEBI
CYTIDINE-5'-diphosphATE	ChEBI
Cytidine 5'-pyrophosphoric acid	Generator
Cytidine diphosphoric acid	Generator
Cytidine, 5'-(trihydrogen pyrophosphoric acid)	Generator
CYTIDINE-5'-diphosphoric acid	Generator
Cytidine-diphosphate	HMDB
Diphosphate, cytidine	HMDB

Chemical Formula

C₉H₁₅N₃O₁₁P₂

Average Molecular Weight

403.1764

Monoisotopic Molecular Weight

403.018181361

IUPAC Name

[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

CDP

CAS Registry Number

63-38-7

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

ZWIADYZPOWUWEW-XVFCMESISA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside diphosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside diphosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Organic pyrophosphate
Monosaccharide phosphate
Monoalkyl phosphate
Pyrimidone
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

cytidine 5'-phosphate (CHEBI:17239 )
pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17239 )
Ribonucleotides (C00112 )

Ontology

Status

Detected but not Quantified

Origin

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	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	-1.4	ALOGPS
logP	-3.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	-0.033	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	221.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	76.29 m³·mol⁻¹	ChemAxon
Polarizability	31.39 Å³	ChemAxon
Number of Rings	2	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	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-5923000000-f7e7b227d8dab9e29e4b	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00di-3209010000-ff27ee45250db3e35193	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-004i-9000000000-f5d958a3ccf576052a6b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-00di-0390000000-0274cdf4190792442001	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0udi-0009000000-2c8a9272dc29076a6167	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0kdi-9602700000-4b46ddc9506634a02dc5	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-0a4i-0059000000-d598d99a604dda402181	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0udi-0003900000-69398917fb0c37a4304f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0zg0-0726900000-8d967e8ca6677a467fb8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-0k9i-0927400000-86e5ba01091f928ca88f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0kdi-9814400000-54042f12a186a46a5a17	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-0k9i-0927400000-61338365caaf6cc96edd	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-03di-0900000000-2e5da7181d5154fd5287	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-056r-8913200000-d327869c80aa6b6ba8b7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-056r-7913200000-4f2656e2010a4274c652	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-ae7cefa275aa112f8ff3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0000900000-1f74a916c1bec3408d2e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-056r-9601000000-0261d005e8d3964fc255	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-056r-8913200000-3093e23d54c628f19ea0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901000000-6aed044cc4135aa261df	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-3900000000-92fac6a8baf47bac3014	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-5ad7bca4dc732a0e3840	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0903300000-44d24cfda26f8f0a8d96	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9701000000-d96a23308bcfcf9cf55f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-d7e0d2a5e8d20180b483	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0100900000-fd8a10c051d8566d4abc	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9418200000-cd847d00773e220445dd	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum