Showing metabocard for dCMP (BMDB0001202)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (6) Show 6 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:42:33 UTC
Update Date2020-05-21 16:29:01 UTC
BMDB IDBMDB0001202
Secondary Accession Numbers
  • BMDB01202
Metabolite Identification
Common NamedCMP
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
ValueSource
2'-Deoxycytidine 5'-monophosphateChEBI
2'-DEOXYCYTIDINE-5'-monophosphATEChEBI
Deoxycytidine monophosphateChEBI
DeoxycytidylateChEBI
Deoxycytidylic acidChEBI
2'-Deoxycytidine 5'-monophosphoric acidGenerator
2'-DEOXYCYTIDINE-5'-monophosphoric acidGenerator
Deoxycytidine monophosphoric acidGenerator
2'-Deoxycytosine 5'-monophosphateHMDB
2'-Deoxycytosine 5'-monophosphoric acidHMDB
2'-Deoxycytidine-3'-monophosphateHMDB
2'-Deoxycytidine-5'-monophosphorateHMDB
2'-Deoxycytidine-5'-phosphateHMDB
Deoxycytidine-phosphateHMDB
Acid, deoxycytidylicHMDB
Deoxycytidylic acidsHMDB
Acids, deoxycytidylicHMDB
monoPhosphate, deoxycytidineHMDB
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 KeyNCMVOABPESMRCP-SHYZEUOFSA-N
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
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Lysosome
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
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 Spectrum (1D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Lysosome
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001202
DrugBank IDDB03798
Phenol Explorer Compound IDNot Available
FooDB IDFDB022488
KNApSAcK IDNot Available
Chemspider ID13343
KEGG Compound IDC00239
BioCyc IDDCMP
BiGG ID34352
Wikipedia LinkDCMP
METLIN ID6078
PubChem Compound13945
PDB IDNot Available
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)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Cytosolic purine 5'-nucleotidase
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:
O46411
Molecular weight:
64841.0
Reactions
dCMP + Water → Deoxycytidine + Hydrogen phosphatedetails
Enzyme Details
2. Uridine-cytidine kinase 1
General function:
Nucleotide transport and metabolism
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor (By similarity).
Gene Name:
UCK1
Uniprot ID:
Q0P5A4
Molecular weight:
31195.0
Reactions
Deoxycytidine + Adenosine triphosphate → dCMP + ADPdetails
Enzyme Details
3. dCTP pyrophosphatase 1
General function:
Involved in dCTP diphosphatase activity
Specific function:
Hydrolyzes deoxynucleoside triphosphates (dNTPs) to the corresponding nucleoside monophosphates. Has a strong preference for dCTP and its analogs including 5-iodo-dCTP and 5-methyl-dCTP for which it may even have a higher efficiency. May protect DNA or RNA against the incorporation of these genotoxic nucleotide analogs through their catabolism.
Gene Name:
DCTPP1
Uniprot ID:
Q32KY6
Molecular weight:
18626.0
Enzyme Details
4. Deoxycytidine kinase
General function:
Nucleotide transport and metabolism
Specific function:
Phosphorylates the deoxyribonucleosides deoxycytidine, deoxyguanosine and deoxyadenosine.
Gene Name:
DCK
Uniprot ID:
Q3MHR2
Molecular weight:
30329.0
Enzyme Details
5. DCTD protein
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
DCTD
Uniprot ID:
A6QQC3
Molecular weight:
20039.0
Reactions
dCMP + Water → dUMP + Ammoniadetails
Enzyme Details
6. Cytidine/uridine monophosphate kinase 2
General function:
Not Available
Specific function:
Not Available
Gene Name:
CMPK2
Uniprot ID:
F1N2W6
Molecular weight:
64396.0
Reactions
dCMP + Adenosine triphosphate → dCDP + ADPdetails