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Record Information |
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Version | 4.0 |
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Status | Detected and Quantified |
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Creation Date | 2005-11-16 15:48:42 UTC |
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Update Date | 2020-09-15 18:43:18 UTC |
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HMDB ID | HMDB0001546 |
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Secondary Accession Numbers | |
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Metabolite Identification |
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Common Name | CDP |
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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. |
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Structure | |
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Synonyms | Value | Source |
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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 |
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Chemical Formula | C9H15N3O11P2 |
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Average Molecular Weight | 403.1764 |
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Monoisotopic Molecular Weight | 403.018181361 |
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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 |
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Traditional Name | CDP |
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CAS Registry Number | 63-38-7 |
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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 |
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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 |
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InChI Key | ZWIADYZPOWUWEW-XVFCMESISA-N |
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Chemical Taxonomy |
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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. |
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Kingdom | Organic compounds |
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Super Class | Nucleosides, nucleotides, and analogues |
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Class | Pyrimidine nucleotides |
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Sub Class | Pyrimidine ribonucleotides |
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Direct Parent | Pyrimidine ribonucleoside diphosphates |
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Alternative Parents | |
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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
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Molecular Framework | Aromatic heteromonocyclic compounds |
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External Descriptors | |
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Ontology |
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Disposition | Route of exposure: Source: Biological location: |
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Process | Naturally occurring process: |
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Role | Industrial application: |
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Physical Properties |
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State | Solid |
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Experimental Properties | Property | Value | Reference |
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Melting Point | Not Available | Not Available | Boiling Point | Not Available | Not Available | Water Solubility | Not Available | Not Available | LogP | 2.44 | HANSCH,C ET AL. (1995) |
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Predicted Properties | |
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Spectra |
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| Spectrum Type | Description | Splash Key | View |
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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 | 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 | 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 | 1D NMR | 1H NMR Spectrum | Not Available | Spectrum | 1D NMR | 13C NMR Spectrum | Not Available | Spectrum |
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Biological Properties |
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Cellular Locations | |
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Biospecimen Locations | |
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Tissue Locations | Not Available |
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Pathways | |
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Normal Concentrations |
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Blood | Detected and Quantified | 36.0 +/- 12.0 uM | Adult (>18 years old) | Both | Normal | | details |
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Abnormal Concentrations |
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| Not Available |
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Associated Disorders and Diseases |
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Disease References | None |
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Associated OMIM IDs | None |
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External Links |
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DrugBank ID | DB04555 |
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Phenol Explorer Compound ID | Not Available |
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FooDB ID | FDB022683 |
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KNApSAcK ID | Not Available |
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Chemspider ID | 5902 |
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KEGG Compound ID | C00112 |
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BioCyc ID | CDP |
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BiGG ID | 33901 |
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Wikipedia Link | Cytidine_diphosphate |
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METLIN ID | 6313 |
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PubChem Compound | 6132 |
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PDB ID | Not Available |
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ChEBI ID | 17239 |
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Food Biomarker Ontology | Not Available |
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VMH ID | CDP |
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MarkerDB ID | |
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References |
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Synthesis Reference | Chambers, Robert Warner; Shapiro, Philip; Kurkov, Viktor. Synthesis of cytidine 5'-diphosphate and guanosine 5'-diphosphate. Journal of the American Chemical Society (1960), 82 970-5. |
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Material Safety Data Sheet (MSDS) | Not Available |
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General References | - George TP, Cook HW, Byers DM, Palmer FB, Spence MW: Inhibition of phosphatidylcholine and phosphatidylethanolamine biosynthesis by cytochalasin B in cultured glioma cells: potential regulation of biosynthesis by Ca(2+)-dependent mechanisms. Biochim Biophys Acta. 1991 Jul 9;1084(2):185-93. [PubMed:1854804 ]
- Riekhof WR, Voelker DR: Uptake and utilization of lyso-phosphatidylethanolamine by Saccharomyces cerevisiae. J Biol Chem. 2006 Dec 1;281(48):36588-96. Epub 2006 Oct 2. [PubMed:17015438 ]
- Tsitolovskii LE, Kraevskii AA: [Possible relation between learning and non-template RNA synthesis in neurons]. Zh Vyssh Nerv Deiat Im I P Pavlova. 1982 Mar-Apr;32(2):284-91. [PubMed:6178232 ]
- Houtkooper RH, Akbari H, van Lenthe H, Kulik W, Wanders RJ, Frentzen M, Vaz FM: Identification and characterization of human cardiolipin synthase. FEBS Lett. 2006 May 29;580(13):3059-64. Epub 2006 Apr 27. [PubMed:16678169 ]
- Carstensen S, Pliska-Matyshak G, Bhuvarahamurthy N, Robbins KM, Murthy PP: Biosynthesis and localization of phosphatidyl-scyllo-inositol in barley aleurone cells. Lipids. 1999 Jan;34(1):67-73. [PubMed:10188599 ]
- Nowicki M, Muller F, Frentzen M: Cardiolipin synthase of Arabidopsis thaliana. FEBS Lett. 2005 Apr 11;579(10):2161-5. [PubMed:15811335 ]
- George TP, Morash SC, Cook HW, Byers DM, Palmer FB, Spence MW: Phosphatidylcholine biosynthesis in cultured glioma cells: evidence for channeling of intermediates. Biochim Biophys Acta. 1989 Aug 22;1004(3):283-91. [PubMed:2758024 ]
- Houtkooper RH, Vaz FM: Cardiolipin, the heart of mitochondrial metabolism. Cell Mol Life Sci. 2008 Aug;65(16):2493-506. doi: 10.1007/s00018-008-8030-5. [PubMed:18425414 ]
- Lindblad L, Schersten T: Incorporation rate in vitro of choline and methyl-methionine into human hepatic lecithins. Scand J Gastroenterol. 1976;11(6):587-91. [PubMed:981963 ]
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