General Information of MET (ID: META00155)
Name Cytidine
Synonyms   Click to Show/Hide Synonyms of This Metabolite
1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine; 1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine; 1-b-D-Ribosyl-cytosine; 1-beta-D-Ribofuranosyl-cytosine; 1-beta-D-Ribofuranosylcytosine; 1-beta-delta-Ribofuranosyl-cytosine; 1-beta-delta-Ribofuranosylcytosine; 1-beta-delta-Ribosyl-cytosine; 1beta-D-Ribofuranosylcytosine; 1beta-Ribofuranosylcytosine; 1beta-delta-Ribofuranosylcytosine; 4-AMINO-1-BETA-D-ribofuranosyl-2(1H)-pyrimidinone; 4-Amino-1-beta-D-ribofuranosylpyrimidin-2(1H)-one; 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone; 4-Amino-1beta-D-ribofuranosyl-2(1H)-pyrimidinone; Cyd; Cytidin; Cytosine ribonucleoside; Cytosine riboside; Cytosine-1b-delta-ribofuranoside; Cytosine-1beta-D-ribofuranoside; Cytosine-1beta-delta-ribofuranoside; Posilent; Ribonucleoside, cytosine; Riboside, cytosine; Zytidin
Source Endogenous;Escherichia Coli Metabolite;Yeast Metabolite;Food;Drug;Cosmetic;TCM Ingredients;Microbial
Structure Type   Pyrimidine nucleosides  (Click to Show/Hide the Complete Structure Type Hierarchy)
Nucleosides, nucleotides, and analogues
Pyrimidine nucleosides
PubChem CID
6175
HMDB ID
HMDB0000089
Formula
C9H13N3O5
Structure
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3D MOL 2D MOL
  Click to Show/Hide the Molecular/Functional Data (External Links/Property/Function) of This Metabolite
KEGG ID
C00475
DrugBank ID
DB02097
ChEBI ID
17562
FooDB ID
FDB021809
ChemSpider ID
5940
METLIN ID
3376
Physicochemical Properties Molecular Weight 243.22 Topological Polar Surface Area 129
XlogP -2.1 Complexity 383
Heavy Atom Count 17 Rotatable Bond Count 2
Hydrogen Bond Donor Count 4 Hydrogen Bond Acceptor Count 5
Function
Cytidine is a nucleoside that is composed of the base cytosine linked to the five-carbon sugar D-ribose. Cytidine is a pyrimidine that besides being incorporated into nucleic acids, can serve as a substrate for the salvage pathway of pyrimidine nucleotide synthesis. It is a precursor of cytidine triphosphate (CTP) needed in the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthetic pathways. These variations probably reflect the species differences in cytidine deaminase, the enzyme that converts cytidine to uridine in the body. The transport of cytidine into the brain's extracellular fluid, and then into neurons and glia, are essential prerequisites for cytidine to be utilized in the brain. An efficient mechanism mediating the brain uptake of circulating cytidine has not yet been demonstrated. The biosynthesis of PC, the most abundant phosphatide in the brain, via the Kennedy pathway requires phosphocholine and cytidine triphosphate (CTP), a cytidine nucleotide involved in the rate-limiting step. The enzyme that converts CTP to endogenous CDP-choline (CTP:phosphocholine cytidylyltransferase) is unsaturated at physiological brain CTP levels. APOBEC is a family of enzymes that has been discovered with the ability to deaminate cytidines on RNA or DNA. The human apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G protein (APOBEC3G, or hA3G), provides cells with an intracellular antiretroviral activity that is associated with the hypermutation of viral DNA through cytidine deamination. Indeed, hA3G belongs to a family of vertebrate proteins that contains one or two copies of a signature sequence motif unique to cytidine deaminases (CTDAs).
Regulatory Network
Full List of Protein(s) Regulating This Metabolite
      Hydrolases (EC 3)
            Sulfatase sulf-1 (SULF1) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [1]
                      Introduced Variation Knockdown (shRNA) of SULF1
                      Induced Change Cytidine concentration: decrease (FC = 0.16 / 0.21)
                      Summary Introduced Variation         Induced Change 
                      Disease Status Ovarian cancer [ICD-11: 2C73]
                      Details It is reported that knockdown of SULF1 leads to the decrease of cytidine levels compared with control group.
      Nitrogen permease regulator (NPR)
            Natriuretic peptide receptor B (NPR2) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [2]
                      Introduced Variation Deletion of NPR2
                      Induced Change Cytidine concentration: increase
                      Summary Introduced Variation         Induced Change 
                      Disease Status Healthy individual
                      Details It is reported that deletion of NPR2 leads to the increase of cytidine levels compared with control group.
      Oxidoreductases (EC 1)
            Glutamate-cysteine ligase modifier (GCLM) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [3]
                      Introduced Variation Knockout of Gclm
                      Induced Change Cytidine concentration: increase (FC = 1.60)
                      Summary Introduced Variation         Induced Change 
                      Disease Status Metabolic liver disease [ICD-11: 5C90]
                      Details It is reported that knockout of Gclm leads to the increase of cytidine levels compared with control group.
      Pore-forming PNC peptide (PNC)
            Cellular tumor antigen p53 (TP53) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [4]
                      Introduced Variation Knockout of TP53
                      Induced Change Cytidine concentration: increase (Log2 FC=7.28)
                      Summary Introduced Variation         Induced Change 
                      Disease Status Colon cancer [ICD-11: 2B90]
                      Details It is reported that knockout of TP53 leads to the increase of cytidine levels compared with control group.
References
1 Erratum to: Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer. Cancer Metab. 2014 Nov 4;2:24.
2 Npr2 inhibits TORC1 to prevent inappropriate utilization of glutamine for biosynthesis of nitrogen-containing metabolites. Sci Signal. 2014 Dec 16;7(356):ra120.
3 Hepatic metabolic adaptation in a murine model of glutathione deficiency. Chem Biol Interact. 2019 Apr 25;303:1-6.
4 Integrative omics analysis of p53-dependent regulation of metabolism. FEBS Lett. 2018 Feb;592(3):380-393.

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