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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:04:01 UTC
HMDB IDHMDB01202
Secondary Accession NumbersNone
Metabolite Identification
Common NamedCMP
DescriptionDeoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions. Deficiency of the enzyme Deoxycytidine kinase (EC 2.7.1.74) is associated with resistance to antiviral and anticancer chemotherapeutic agents, whereas increased enzyme activity is associated with increased activation of these compounds to cytotoxic nucleoside triphosphate derivatives. (OMIM 125450 ).
Structure
Thumb
Synonyms
ValueSource
2'-Deoxycytidine 5'-monophosphateChEBI
2'-DEOXYCYTIDINE-5'-monophosphATEChEBI
2'-Deoxycytosine 5'-monophosphateChEBI
Deoxycytidine monophosphateChEBI
DeoxycytidylateChEBI
Deoxycytidylic acidChEBI
2'-Deoxycytidine 5'-monophosphoric acidGenerator
2'-DEOXYCYTIDINE-5'-monophosphoric acidGenerator
2'-Deoxycytosine 5'-monophosphoric acidGenerator
Deoxycytidine monophosphoric acidGenerator
2'-Deoxycytidine-3'-monophosphateHMDB
2'-Deoxycytidine-5'-monophosphorateHMDB
2'-Deoxycytidine-5'-phosphateHMDB
Deoxycytidine-phosphateHMDB
Chemical FormulaC9H14N3O7P
Average Molecular Weight307.1971
Monoisotopic Molecular Weight307.056936329
IUPAC Name{[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional NamedCMP
CAS Registry Number1032-65-1
SMILES
NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
InChI Identifier
InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChI KeyInChIKey=NCMVOABPESMRCP-SHYZEUOFSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Monoalkyl phosphate
  • Pyrimidone
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
Biofunction
  • Component of Nicotinate and nicotinamide metabolism
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility10.9 mg/mLALOGPS
logP-2.1ALOGPS
logP-2.6ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.26ChemAxon
pKa (Strongest Basic)-0.12ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area154.91 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity63.91 m3·mol-1ChemAxon
Polarizability26.2 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-0900000000-01bb64efeca205daaf6eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-1900000000-13c56ec900e188e10ddbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-03di-5900000000-4e6dd8fdc8a4142269a2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid LocationsNot Available
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Beta Ureidopropionase DeficiencySMP00172Not Available
Dihydropyrimidinase DeficiencySMP00178Not Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)SMP00202Not Available
Pyrimidine MetabolismSMP00046map00240
UMP Synthase Deiciency (Orotic Aciduria)SMP00219Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022488
KNApSAcK IDNot Available
Chemspider ID13343
KEGG Compound IDC00239
BioCyc IDDCMP
BiGG ID34352
Wikipedia LinkdCMP
NuGOwiki LinkHMDB01202
Metagene LinkHMDB01202
METLIN ID6078
PubChem Compound13945
PDB IDDC
ChEBI ID15918
References
Synthesis ReferenceTanaka, Toshiki; Yamada, Yasuki; Ikehara, Morio. Chemical synthesis of deoxyribonucleotide with a 5'-phosphoryl group on a polystyrene polymer support by the phosphotriester method. Chemical & Pharmaceutical Bulletin (1987), 35(7), 2726-33.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Itoh K, Aida S, Ishiwata S, Yamaguchi T, Ishida N, Mizugaki M: Immunochemical detection of urinary 5-methyl-2'-deoxycytidine as a potential biologic marker for leukemia. Clin Chim Acta. 1995 Jan 31;234(1-2):37-45. [7758221 ]
  2. Mills GC, Schmalstieg FC, Goldblum RM: Urinary excretion of modified purines and nucleosides in immunodeficient children. Biochem Med. 1985 Aug;34(1):37-51. [4052062 ]
  3. Chen HJ, Wu CF, Hong CL, Chang CM: Urinary excretion of 3,N4-etheno-2'-deoxycytidine in humans as a biomarker of oxidative stress: association with cigarette smoking. Chem Res Toxicol. 2004 Jul;17(7):896-903. [15257614 ]
  4. Zambonin CG, Aresta A, Palmisano F, Specchia G, Liso V: Liquid chromatographic determination of urinary 5-methyl-2'-deoxycytidine and pseudouridine as potential biological markers for leukaemia. J Pharm Biomed Anal. 1999 Dec;21(5):1045-51. [10703973 ]
  5. Abbruzzese JL, Grunewald R, Weeks EA, Gravel D, Adams T, Nowak B, Mineishi S, Tarassoff P, Satterlee W, Raber MN, et al.: A phase I clinical, plasma, and cellular pharmacology study of gemcitabine. J Clin Oncol. 1991 Mar;9(3):491-8. [1999720 ]
  6. Zambonin CG, Palmisano F: Electrospray ionization mass spectrometry of 5-methyl-2'-deoxycytidine and its determination in urine by liquid chromatography/electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom. 1999;13(21):2160-5. [10523775 ]
  7. Masuda N, Matsui K, Yamamoto N, Nogami T, Nakagawa K, Negoro S, Takeda K, Takifuji N, Yamada M, Kudoh S, Okuda T, Nemoto S, Ogawa K, Myobudani H, Nihira S, Fukuoka M: Phase I trial of oral 2'-deoxy-2'-methylidenecytidine: on a daily x 14-day schedule. Clin Cancer Res. 2000 Jun;6(6):2288-94. [10873079 ]
  8. Broder S: Pharmacodynamics of 2',3'-dideoxycytidine: an inhibitor of human immunodeficiency virus. Am J Med. 1990 May 21;88(5B):2S-7S. [1692446 ]
  9. Chen HJ, Lin TC, Hong CL, Chiang LC: Analysis of 3,N(4)-ethenocytosine in DNA and in human urine by isotope dilution gas chromatography/negative ion chemical ionization/mass spectrometry. Chem Res Toxicol. 2001 Dec;14(12):1612-9. [11743744 ]
  10. Sottani C, Zucchetti M, Zaffaroni M, Bettinelli M, Minoia C: Validated procedure for simultaneous trace level determination of the anti-cancer agent gemcitabine and its metabolite in human urine by high-performance liquid chromatography with tandem mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(10):1017-23. [15150823 ]
  11. Mazurets AF, Kubyshkin VF, Dziuba MV: [The cytochemical characteristics of the blood polymorphonuclear leukocytes in dilated cardiomyopathy and an inflammatory myocardial lesion] Lik Sprava. 1994 Jul-Aug;(7-8):109-12. [7900329 ]
  12. Zegers BJ, Stoop JW, Staal GE, Wadman SK: An approach to the restoration of T cell function in a purine nucleoside phosphorylase deficient patient. Ciba Found Symp. 1978;(68):231-53. [115663 ]
  13. de Bono JS, Stephenson J Jr, Baker SD, Hidalgo M, Patnaik A, Hammond LA, Weiss G, Goetz A, Siu L, Simmons C, Jolivet J, Rowinsky EK: Troxacitabine, an L-stereoisomeric nucleoside analog, on a five-times-daily schedule: a phase I and pharmacokinetic study in patients with advanced solid malignancies. J Clin Oncol. 2002 Jan 1;20(1):96-109. [11773159 ]
  14. Lebedev PA: [Selenium deficiency in patients with cardiovascular diseases and its correction with the drug "selena"] Patol Fiziol Eksp Ter. 1996 Jul-Sep;(3):5-7. [8966057 ]
  15. Shejbal J, Arient M, Kovarikova H: Estimation of deoxycytidine in the urine of humans and laboratory animals. Clin Chim Acta. 1967 May;16(2):324-5. [4962141 ]
  16. Chen IW, Kereiakes JG, Friedman BI, Saenger EL: Colorimetric analysis of deoxycytidine in urine after separation by ion-exchange column chromatography. Anal Biochem. 1968 May;23(2):230-40. [5657794 ]
  17. Dientsbier Z, Buric L, Bechyne M, Kovarikova H, Foltynova V, Mostecky H: Deoxypyrimidineuria in the course of chemotherapy in M. Hodgkin. Neoplasma. 1976;23(6):645-65. [1004661 ]
  18. Dudley E, Lemiere F, Van Dongen W, Langridge JI, El-Sharkawi S, Games DE, Esmans EL, Newton RP: Analysis of urinary nucleosides. III. Identification of 5'-deoxycytidine in urine of a patient with head and neck cancer. Rapid Commun Mass Spectrom. 2003;17(11):1132-6. [12772268 ]
  19. Arient M, Dienstbier Z, Shejbal J: The post-irradiation excretion of deoxycytidine by urine in man. Minerva Fisiconucl. 1966;10(1):57-60. [5956823 ]
  20. Tuma P, Samcova E, Kvasnicova V: Improved detection limit for a direct determination of 8-hydroxy-2'-deoxyguanosine in untreated urine samples by capillary electrophoresis with optical detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Dec 25;813(1-2):255-61. [15556541 ]

Enzymes

General function:
Involved in thymidylate kinase activity
Specific function:
May participate in dUTP and dCTP synthesis in mitochondria. Is able to phosphorylate dUMP, dCMP, CMP, UMP and monophosphates of the pyrimidine nucleoside analogs ddC, dFdC, araC, BVDU and FdUrd with ATP as phosphate donor. Efficacy is highest for dUMP followed by dCMP; CMP and UMP are poor substrates. May be involved in mtDNA depletion caused by long term treatment with ddC or other pyrimidine analogs.
Gene Name:
CMPK2
Uniprot ID:
Q5EBM0
Molecular weight:
44958.27
Reactions
Adenosine triphosphate + dCMP → ADP + dCDPdetails
General function:
Involved in ATP binding
Specific function:
Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:
DCK
Uniprot ID:
P27707
Molecular weight:
30518.315
Reactions
NTP + Deoxycytidine → NDP + dCMPdetails
Adenosine triphosphate + Deoxycytidine → ADP + dCMPdetails
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in magnesium ion binding
Specific function:
Can act both as nucleotidase and as phosphotransferase.
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Molecular weight:
33914.91
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in zinc ion binding
Specific function:
Supplies the nucleotide substrate for thymidylate synthetase.
Gene Name:
DCTD
Uniprot ID:
P32321
Molecular weight:
21013.96
Reactions
dCMP + Water → dUMP + Ammoniadetails
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
P49902
Molecular weight:
64969.2
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
Reactions
dCMP + Water → Deoxycytidine + Phosphoric aciddetails
General function:
Not Available
Specific function:
Hydrolyzes deoxynucleoside triphosphates (dNTPs) to the corresponding nucleoside monophosphates. Has a strong preference for modified dCTP. Activity is highest with 5-iodo-dCTP, followed by 5-bromo-dCTP, unmodified dCTP, 5-methyl-dCTP and 5-chloro-dCTP. Hydrolyzes 2-chloro-dATP and 2-hydroxy-dATP with lower efficiency, and has even lower activity with unmodified dATP, dTTP and dUTP (in vitro). Does not hydrolyze ATP, UTP, ITP, GTP, dADP, dCDP or dGTP. May protect DNA or RNA against the incorporation of non-canonical nucleotide triphosphates. May protect cells against inappropriate methylation of CpG islands by DNA methyltransferases (By similarity).
Gene Name:
DCTPP1
Uniprot ID:
Q9H773
Molecular weight:
18680.645
Reactions
dCTP + Water → dCMP + Pyrophosphatedetails
General function:
Involved in ATP binding
Specific function:
Catalyzes specific phosphoryl transfer from ATP to UMP and CMP.
Gene Name:
CMPK1
Uniprot ID:
P30085
Molecular weight:
20180.12
Reactions
Adenosine triphosphate + dCMP → ADP + dCDPdetails