Record Information
Version2.0
Creation Date2012-05-31 13:47:37 -0600
Update Date2015-09-13 12:56:10 -0600
Secondary Accession Numbers
  • ECMDB01202
Identification
Name:dCMP
DescriptionDeoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.
Structure
Thumb
Synonyms:
  • 2'-Deoxycytidine 5'-monophosphate
  • 2'-Deoxycytidine 5'-monophosphoric acid
  • 2'-Deoxycytidine-3'-monophosphate
  • 2'-Deoxycytidine-3'-monophosphoric acid
  • 2'-Deoxycytidine-5'-monophosphate
  • 2'-Deoxycytidine-5'-monophosphorate
  • 2'-Deoxycytidine-5'-monophosphoric acid
  • 2'-Deoxycytidine-5'-phosphate
  • 2'-Deoxycytidine-5'-phosphoric acid
  • C
  • DCMP
  • Deoxycytidine monophosphate
  • Deoxycytidine monophosphoric acid
  • Deoxycytidine-phosphate
  • Deoxycytidine-phosphoric acid
  • Deoxycytidylate
  • Deoxycytidylic acid
Chemical Formula:C9H14N3O7P
Weight:Average: 307.1971
Monoisotopic: 307.056936329
InChI Key:NCMVOABPESMRCP-SHYZEUOFSA-N
InChI: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
CAS number:1032-65-1
IUPAC Name:{[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:dCMP
SMILES:NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct ParentPyrimidine 2'-deoxyribonucleoside monophosphates
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside monophosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Amine
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility10.9 g/LALOGPS
logP-2.1ALOGPS
logP-2.3ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.28ChemAxon
pKa (Strongest Basic)0.16ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area154.91 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity63.91 m³·mol⁻¹ChemAxon
Polarizability26.2 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9410000000-f31bf162f5f972b9cf42View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-03dm-9522000000-d25b21eb547d23c4886dView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-004j-9402000000-6a9e4b2e32058773f6bfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 35V, negativesplash10-0006-9000000000-3b4572f2c8e51186f7e5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-bc40821757dbbe57a7c2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-9052cfbf31794c457d3bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-004j-9400000000-1f2a185e05aed001e983View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-5209000000-b46ae8ade9397163198aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004j-9300000000-c6505ac4fafc2bc54910View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-2d1a73d09ad4b06da15fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-03fr-3910000000-ee0cc0c7897818415edcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-7e33f3b263e35a18c2e0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9400000000-4ab96ba8107b5f1820a6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-03di-3900000000-56a3ecce668ff56b702cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-0900000000-986f256cdcdf8c8d2f9fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0006-9000000000-d236c094fbaf8d2136b4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-dd904e0c162b36055113View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-4cc5b5143e38514f3010View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-3b0a0a6948a49378ff1cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4900000000-a901f489d4e9b8516bf2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6900000000-d9e59981c244792a2f76View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6r-9367000000-d5c1062e5203ec9699d4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9110000000-20768d2b834097ac11d7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-29f2d493f3f68928488bView in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • 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. Pubmed: 1999720
  • Arient M, Dienstbier Z, Shejbal J: The post-irradiation excretion of deoxycytidine by urine in man. Minerva Fisiconucl. 1966;10(1):57-60. Pubmed: 5956823
  • Broder S: Pharmacodynamics of 2',3'-dideoxycytidine: an inhibitor of human immunodeficiency virus. Am J Med. 1990 May 21;88(5B):2S-7S. Pubmed: 1692446
  • 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. Pubmed: 11743744
  • 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. Pubmed: 15257614
  • 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. Pubmed: 5657794
  • 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. Pubmed: 11773159
  • 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. Pubmed: 1004661
  • 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. Pubmed: 12772268
  • 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. Pubmed: 7758221
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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. Pubmed: 8966057
  • 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. Pubmed: 10873079
  • 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. Pubmed: 7900329
  • Mills GC, Schmalstieg FC, Goldblum RM: Urinary excretion of modified purines and nucleosides in immunodeficient children. Biochem Med. 1985 Aug;34(1):37-51. Pubmed: 4052062
  • 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. Pubmed: 4962141
  • 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. Pubmed: 15150823
  • 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. Pubmed: 15556541
  • 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. Pubmed: 10703973
  • 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. Pubmed: 10523775
  • 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. Pubmed: 115663
Synthesis Reference:Tanaka, 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)
External Links:
ResourceLink
CHEBI ID15918
HMDB IDHMDB01202
Pubchem Compound ID13945
Kegg IDC00239
ChemSpider ID13343
WikipediadCMP
BioCyc IDDCMP
EcoCyc IDDCMP
Ligand ExpoDNR

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 cytidylate kinase activity
Specific function:
ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors
Gene Name:
cmk
Uniprot ID:
P0A6I0
Molecular weight:
24746
Reactions
ATP + (d)CMP = ADP + (d)CDP.
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 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 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 nucleoside-triphosphate diphosphatase activity
Specific function:
Specific function unknown
Gene Name:
mazG
Uniprot ID:
P0AEY3
Molecular weight:
30412
Reactions
ATP + H(2)O = AMP + diphosphate.
General function:
Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:
Catalyzes the hydrolysis of nucleoside triphosphates, with a preference for pyrimidine deoxynucleoside triphosphates (dUTP, dTTP and dCTP)
Gene Name:
nudI
Uniprot ID:
P52006
Molecular weight:
16371
Reactions
Nucleoside triphosphate + H(2)O = nucleoside monophosphate + diphosphate.
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
Specific function:
Specific for pyrimidine substrates. Acts on 5-methyl- dCTP, CTP and dCTP in decreasing order
Gene Name:
nudG
Uniprot ID:
P77788
Molecular weight:
15046
Reactions
CTP + H(2)O = CMP + diphosphate.

Transporters

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