Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB120106
Identification
Name: dCMP
Description:A 2'-deoxyribonucleoside 5'-monophosphate(2−) obtained by deprotonation of the phosphate OH groups of 2'-deoxycytidine 5'-monophosphate (dCMP); major species at pH 7.3.
Structure
Thumb
Synonyms:
  • 2'-deoxycytosine 5'-monophosphate(2−)
  • dCMP
  • dCMP dianion
Chemical Formula: C9H12N3O7P
Average Molecular Weight: 305.183
Monoisotopic Molecular Weight: 307.05695
InChI Key: NCMVOABPESMRCP-SHYZEUOFSA-L
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)/p-2/t5-,6+,8+/m0/s1
CAS number: 1032-65-1
IUPAC Name:2'-deoxy-5'-O-phosphonatocytidine
Traditional IUPAC Name: dCMP
SMILES:C(C2(C(CC(N1(C(N=C(C=C1)N)=O))O2)O))OP([O-])([O-])=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of chemical entities 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.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Nucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
Direct Parent Pyrimidine 2'-deoxyribonucleoside monophosphates
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside monophosphate
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Primary aromatic amine
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Oxolane
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Primary amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Amine
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
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
Biological Properties
Cellular Locations: Not Available
Reactions:
Pathways:
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
References
References:
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • Broder S: Pharmacodynamics of 2',3'-dideoxycytidine: an inhibitor of human immunodeficiency virus. Am J Med. 1990 May 21;88(5B):2S-7S. [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. [11743744 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • Arient M, Dienstbier Z, Shejbal J: The post-irradiation excretion of deoxycytidine by urine in man. Minerva Fisiconucl. 1966;10(1):57-60. [5956823 ]
  • 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 ]
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
METABOLIGHTSMTBLC57566
HMDBHMDB01202
BIGG34352
CHEMSPIDER5414501
CHEBI57566
PUBCHEM7058169
LIGAND-CPDC00239
CAS1032-65-1