Showing metabocard for dCDP (BMDB0001245)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:43:00 UTC
Update Date2020-05-21 16:29:27 UTC
BMDB IDBMDB0001245
Secondary Accession Numbers
  • BMDB01245
Metabolite Identification
Common NamedCDP
DescriptiondCDP, also known as deoxy-CDP, belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. dCDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dCDP exists in all living species, ranging from bacteria to humans. Within cattle, dCDP participates in a number of enzymatic reactions. In particular, dCDP can be biosynthesized from CDP; which is catalyzed by the enzyme ribonucleoside-diphosphate reductase large subunit. In addition, dCDP can be converted into dCTP; which is mediated by the enzyme nucleoside diphosphate kinase 6. In cattle, dCDP is involved in the metabolic pathway called the pyrimidine metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2'-Deoxycytidine 5'-diphosphateChEBI
2'-Deoxycytidine diphosphateChEBI
D-1beta-Ribofuranosylcytosine diphosphateChEBI
Deoxycytidine diphosphateChEBI
2'-Deoxycytidine 5'-diphosphoric acidGenerator
2'-Deoxycytidine diphosphoric acidGenerator
D-1b-Ribofuranosylcytosine diphosphateGenerator
D-1b-Ribofuranosylcytosine diphosphoric acidGenerator
D-1beta-Ribofuranosylcytosine diphosphoric acidGenerator
D-1Β-ribofuranosylcytosine diphosphateGenerator
D-1Β-ribofuranosylcytosine diphosphoric acidGenerator
Deoxycytidine diphosphoric acidGenerator
2'-Deoxy-cytidine 5'-pyrophosphateHMDB
2'-Deoxy-cytidine pyrophosphateHMDB
2'-Deoxycytidine-5'-diphosphateHMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
delta-1beta-Ribofuranosylcytosine diphosphateHMDB
Deoxy-CDPHMDB
Deoxycytidine 5'-diphosphateHMDB
Chemical FormulaC9H15N3O10P2
Average Molecular Weight387.177
Monoisotopic Molecular Weight387.023266739
IUPAC Name[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional NamedCDP
CAS Registry Number800-73-7
SMILES
NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1
InChI Identifier
InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChI KeyFTDHDKPUHBLBTL-SHYZEUOFSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • 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-1.5ALOGPS
logP-2.6ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.79ChemAxon
pKa (Strongest Basic)0.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area201.44 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity74.78 m³·mol⁻¹ChemAxon
Polarizability30.77 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, Positivesplash10-002e-7912000000-ef0991eaee32b505e016View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0006-9851100000-62426a0730b483cea09bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0570-9418000000-2d9af3073a3dc2deba5dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-056r-9511000000-84defb0c7de79c169ebfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-0409000000-e5af2ab8466aa7c560d3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-0903000000-1de5fa4ac24e19830f39View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-000i-0009000000-4aa3ce1bf37251d7fc83View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-056r-9435000000-55592321586c623c4830View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0a4i-0903000000-1de5fa4ac24e19830f39View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-056r-9411000000-84bbde6c497548c746d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-63f9c6b289fb024c58faView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-e584f4f2cb1a8a01a7e7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3910000000-d34603d21a6d1d52ae1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-52ac41f181e1d5fbf96aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000f-4209000000-ea241dab90201ce7963eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9601000000-55120f468bf1ebba66cdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-bd81788fb13a599a4f60View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-63028e00ccb9887f46f5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-9b943638c706a10be8dbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3910000000-f5ebfcca0e4ec5d76afaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0409000000-47d71d5707b30d7b3ad5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9324000000-25bfbc45e3248b83b219View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 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, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001245
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022510
KNApSAcK IDNot Available
Chemspider ID132961
KEGG Compound IDC00705
BioCyc IDDCDP
BiGG ID50858
Wikipedia LinkDeoxycytidine_diphosphate
METLIN ID6105
PubChem Compound150855
PDB IDNot Available
ChEBI ID28846
References
Synthesis ReferenceNara, Takashi; Misawa, Masanaru. Bacterial phosphorylation of 5'-deoxycytidine monophosphate to di-or triphosphate. Jpn. Tokkyo Koho (1971), 2 pp.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Nucleoside diphosphate kinase 7
General function:
Nucleotide transport and metabolism
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
Gene Name:
NME7
Uniprot ID:
Q5E9Y9
Molecular weight:
42599.0
Reactions
dCDP + Adenosine triphosphate → dCTP + ADPdetails
Enzyme Details
2. 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
Enzyme Details
3. Ribonucleotide reductase regulatory subunit M2
General function:
Not Available
Specific function:
Not Available
Gene Name:
RRM2
Uniprot ID:
E1BI58
Molecular weight:
44821.0
Reactions
CDP + thioredoxin disulfide + Water → dCDP + thioredoxindetails