dCMP (YMDB00206)

Identification
YMDB IDYMDB00206
NamedCMP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptiondCMP, also known as deoxycytidylate, 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. dCMP is an extremely weak basic (essentially neutral) compound (based on its pKa). dCMP exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2'-Deoxycytidine 5'-monophosphate
  • 2'-Deoxycytidine-3'-monophosphate
  • 2'-Deoxycytidine-5'-monophosphate
  • 2'-Deoxycytidine-5'-monophosphorate
  • 2'-Deoxycytidine-5'-monophosphoric acid
  • 2'-deoxycytidine-5'-phosphate
  • dCMP
  • deoxycytidine monophosphate
  • deoxycytidine-phosphate
  • Deoxycytidylate
  • deoxycytidylic acid
  • 2'-Deoxycytidine 5'-monophosphoric acid
  • Deoxycytidine monophosphoric acid
  • 2'-Deoxycytosine 5'-monophosphate
  • 2'-Deoxycytosine 5'-monophosphoric acid
  • Acid, deoxycytidylic
  • Deoxycytidylic acids
  • Acids, deoxycytidylic
  • monoPhosphate, deoxycytidine
CAS number1032-65-1
WeightAverage: 307.1971
Monoisotopic: 307.056936329
InChI KeyNCMVOABPESMRCP-SHYZEUOFSA-N
InChIInChI=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
IUPAC Name{[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC NamedCMP
Chemical FormulaC9H14N3O7P
SMILES[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(=O)(O[H])O[H])N1C([H])=C([H])C(=NC1=O)N([H])[H]
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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
water + dCMP → phosphate + 2'-Deoxycytidine
Adenosine triphosphate + dCMP ↔ dCDP + ADP
water + hydron + dCMP ↔ dUMP + Ammonium
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9410000000-f31bf162f5f972b9cf42JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-03dm-9522000000-d25b21eb547d23c4886dJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-0900000000-01bb64efeca205daaf6eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-1900000000-13c56ec900e188e10ddbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-03di-5900000000-4e6dd8fdc8a4142269a2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-004j-9402000000-6a9e4b2e32058773f6bfJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 35V, negativesplash10-0006-9000000000-3b4572f2c8e51186f7e5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-bc40821757dbbe57a7c2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-9052cfbf31794c457d3bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-004j-9400000000-1f2a185e05aed001e983JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-5209000000-b46ae8ade9397163198aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004j-9300000000-c6505ac4fafc2bc54910JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-2d1a73d09ad4b06da15fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-03fr-3910000000-ee0cc0c7897818415edcJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-7e33f3b263e35a18c2e0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9400000000-4ab96ba8107b5f1820a6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-03di-3900000000-56a3ecce668ff56b702cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-03di-0900000000-986f256cdcdf8c8d2f9fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0006-9000000000-d236c094fbaf8d2136b4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-dd904e0c162b36055113JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-4cc5b5143e38514f3010JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-3b0a0a6948a49378ff1cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4900000000-a901f489d4e9b8516bf2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6900000000-d9e59981c244792a2f76JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6r-9367000000-d5c1062e5203ec9699d4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9110000000-20768d2b834097ac11d7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-29f2d493f3f68928488bJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). "The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism." BMC Syst Biol 2:71.18687109
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.
External Links:
ResourceLink
CHEBI ID15918
HMDB IDHMDB01202
Pubchem Compound ID13945
Kegg IDC00239
ChemSpider ID25057310
FOODB IDFDB022488
WikipediaDeoxycytidine_monophosphate
BioCyc IDDCMP

Enzymes

Protein Details
1. Deoxycytidylate deaminase
General function:
Involved in zinc ion binding
Specific function:
Supplies the nucleotide substrate for thymidylate synthetase
Gene Name:
DCD1
Uniprot ID:
P06773
Molecular weight:
35645.69922
Reactions
dCMP + H(2)O → dUMP + NH(3).