Cytidine (ECMDB00089) (M2MDB000033)
Record Information | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Version | 2.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Creation Date | 2012-05-31 09:57:04 -0600 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Update Date | 2015-09-13 12:56:06 -0600 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Secondary Accession Numbers |
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Identification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Name: | Cytidine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Description | 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 substrate for the salvage pathway of pyrimidine nucleotide synthesis; as precursor of the cytidine triphosphate (CTP) needed in the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthetic pathway. These variations probably reflect the species differences in cytidine deaminase. The biosynthesis of PC via the Kennedy pathway requires phosphocholine and cytidine triphosphate (CTP), a cytidine nucleotide, which is involved in the rate-limiting step. (PMID: 16769123, 15780864, 16720547) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Synonyms: |
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Chemical Formula: | C9H13N3O5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Weight: | Average: 243.2166 Monoisotopic: 243.085520541 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
InChI Key: | UHDGCWIWMRVCDJ-XVFCMESISA-N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
InChI: | InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CAS number: | 65-46-3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IUPAC Name: | 4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Traditional IUPAC Name: | cytarabine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMILES: | NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Chemical Taxonomy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Description | belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Kingdom | Organic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Super Class | Nucleosides, nucleotides, and analogues | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Class | Pyrimidine nucleosides | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sub Class | Not Available | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Direct Parent | Pyrimidine nucleosides | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Alternative Parents | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Substituents |
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Molecular Framework | Aromatic heteromonocyclic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
External Descriptors |
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Physical Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
State: | Solid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Charge: | 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Melting point: | 230.5 °C | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Experimental Properties: |
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Predicted Properties |
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Biological Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Cellular Locations: | Cytoplasm | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reactions: | Cytidine monophosphate + Water > Cytidine + Phosphate Cytidine + Water > Cytosine + Ribose Cytidine + Guanosine triphosphate > Cytidine monophosphate + Guanosine diphosphate + Hydrogen ion Cytidine + Hydrogen ion + Water > Ammonium + Uridine 3'-CMP + Water > Cytidine + Phosphate Cytidine monophosphate + Water <> Cytidine + Phosphate Adenosine triphosphate + Cytidine <> ADP + Cytidine monophosphate Uridine triphosphate + Cytidine <> Uridine 5'-diphosphate + Cytidine monophosphate Guanosine triphosphate + Cytidine <> Guanosine diphosphate + Cytidine monophosphate Inosine triphosphate + Cytidine <> IDP + Cytidine monophosphate dATP + Cytidine <> dADP + Cytidine monophosphate Cytidine + Water <> Uridine + Ammonia dGTP + Cytidine <> dGDP + Cytidine monophosphate Thymidine 5'-triphosphate + Cytidine <> dTDP + Cytidine monophosphate Cytidine + Water <> Cytosine + Ribose dCTP + Cytidine <> dCDP + Cytidine monophosphate Deoxyuridine triphosphate + Cytidine <> dUDP + Cytidine monophosphate Water + Cytidine > Ammonia + Uridine Cytidine + Water > D-ribose + Cytosine Adenosine triphosphate + Cytidine > ADP + Cytidine monophosphate Cytidine + Water + Deoxycytidine <> Uridine + Ammonia + Deoxyuridine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMPDB Pathways: |
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KEGG Pathways: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EcoCyc Pathways: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Concentrations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Find out more about how we convert literature concentrations. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Spectra | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Spectra: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
References | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
References: |
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Synthesis Reference: | Qu, Guirong; Yang, Xining; Shen, Yanhong; Dong, Chunhong; Guo, Haiming; Wang, Xiuqiang; Wang, Dongchao. Synthesis of cytidine. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 11pp. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Material Safety Data Sheet (MSDS) | Download (PDF) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Links | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
External Links: |
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Enzymes
- General function:
- Involved in hydrolase activity
- Specific function:
- Degradation of external UDP-glucose to uridine monophosphate and glucose-1-phosphate, which can then be used by the cell
- Gene Name:
- ushA
- Uniprot ID:
- P07024
- Molecular weight:
- 60824
Reactions
UDP-sugar + H(2)O = UMP + alpha-D-aldose 1-phosphate. |
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate. |
- General function:
- Involved in hydrolase activity
- Specific function:
- This bifunctional enzyme catalyzes two consecutive reactions during ribonucleic acid degradation. Converts a 2',3'- cyclic nucleotide to a 3'-nucleotide and then the 3'-nucleotide to the corresponding nucleoside and phosphate
- Gene Name:
- cpdB
- Uniprot ID:
- P08331
- Molecular weight:
- 70832
Reactions
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate. |
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate. |
- General function:
- Involved in hydrolase activity
- Specific function:
- Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of E.coli in stationary growth phase
- Gene Name:
- surE
- Uniprot ID:
- P0A840
- Molecular weight:
- 26900
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate. |
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate. |
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate. |
- General function:
- Involved in ATP binding
- Specific function:
- ATP + uridine = ADP + UMP
- Gene Name:
- udk
- Uniprot ID:
- P0A8F4
- Molecular weight:
- 24353
Reactions
ATP + uridine = ADP + UMP. |
ATP + cytidine = ADP + CMP. |
- General function:
- Involved in catalytic activity
- Specific function:
- Nucleotidase that shows high phosphatase activity toward three nucleoside 5'-monophosphates, UMP, dUMP, and dTMP, and very low activity against TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6- phosphogluconate. Is strictly specific to substrates with 5'- phosphates and shows no activity against nucleoside 2'- or 3'- monophosphates. Might be involved in the pyrimidine nucleotide substrate cycles
- Gene Name:
- yjjG
- Uniprot ID:
- P0A8Y1
- Molecular weight:
- 25300
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate. |
- General function:
- Involved in zinc ion binding
- Specific function:
- This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis
- Gene Name:
- cdd
- Uniprot ID:
- P0ABF6
- Molecular weight:
- 31539
Reactions
Cytidine + H(2)O = uridine + NH(3). |
- General function:
- Involved in acid phosphatase activity
- Specific function:
- Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
- Gene Name:
- aphA
- Uniprot ID:
- P0AE22
- Molecular weight:
- 26103
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate. |
- General function:
- Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
- Specific function:
- Hydrolyzes both purine and pyrimidine ribonucleosides with a broad-substrate specificity with decreasing activity in the order uridine, xanthosine, inosine, adenosine, cytidine, guanosine
- Gene Name:
- rihC
- Uniprot ID:
- P22564
- Molecular weight:
- 32560
- General function:
- Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
- Specific function:
- Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides. Has a low but significant activity for the purine nucleoside xanthosine
- Gene Name:
- rihB
- Uniprot ID:
- P33022
- Molecular weight:
- 33748
Reactions
A pyrimidine nucleoside + H(2)O = D-ribose + a pyrimidine base. |
- General function:
- Involved in catalytic activity
- Specific function:
- Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli
- Gene Name:
- yfbR
- Uniprot ID:
- P76491
- Molecular weight:
- 22708
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate. |
- General function:
- Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
- Specific function:
- Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively
- Gene Name:
- rihA
- Uniprot ID:
- P41409
- Molecular weight:
- 33823
Transporters
- General function:
- Involved in nucleoside transmembrane transporter activity
- Specific function:
- Nucleoside transport
- Gene Name:
- xapB
- Uniprot ID:
- P45562
- Molecular weight:
- 46139
- General function:
- Involved in nucleoside:sodium symporter activity
- Specific function:
- Transports nucleosides with a high affinity except guanosine and deoxyguanosine. Driven by a proton motive force
- Gene Name:
- nupC
- Uniprot ID:
- P0AFF2
- Molecular weight:
- 43475
- General function:
- Involved in nucleoside transmembrane transporter activity
- Specific function:
- Transports nucleosides with a high affinity. Driven by a proton motive force
- Gene Name:
- nupG
- Uniprot ID:
- P0AFF4
- Molecular weight:
- 46389
- General function:
- Involved in nucleoside:sodium symporter activity
- Specific function:
- Nucleoside transporter
- Gene Name:
- nupX
- Uniprot ID:
- P33021
- Molecular weight:
- 43409
- General function:
- Involved in transporter activity
- Specific function:
- Non-specific porin
- Gene Name:
- ompN
- Uniprot ID:
- P77747
- Molecular weight:
- 41220
- General function:
- Involved in transporter activity
- Specific function:
- Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
- Gene Name:
- phoE
- Uniprot ID:
- P02932
- Molecular weight:
- 38922
- General function:
- Involved in transporter activity
- Specific function:
- OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
- Gene Name:
- ompF
- Uniprot ID:
- P02931
- Molecular weight:
- 39333
- General function:
- Involved in transporter activity
- Specific function:
- Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
- Gene Name:
- ompC
- Uniprot ID:
- P06996
- Molecular weight:
- 40368