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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:43:01 UTC
Update Date2021-09-24 07:43:01 UTC
HMDB IDHMDB0304166
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Description4-diphosphocytidyl-2-c-methyl-d-erythritol is a member of the class of compounds known as pyrimidine ribonucleoside diphosphates. Pyrimidine ribonucleoside diphosphates are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. 4-diphosphocytidyl-2-c-methyl-d-erythritol is soluble (in water) and a moderately acidic compound (based on its pKa). 4-diphosphocytidyl-2-c-methyl-d-erythritol can be found in a number of food items such as pepper (c. chinense), pistachio, chestnut, and lupine, which makes 4-diphosphocytidyl-2-c-methyl-d-erythritol a potential biomarker for the consumption of these food products. 4-diphosphocytidyl-2-c-methyl-d-erythritol may be a unique E.coli metabolite.
Structure
Thumb
SynonymsNot Available
Chemical FormulaC14H25N3O14P2
Average Molecular Weight521.3075
Monoisotopic Molecular Weight521.081175547
IUPAC Name[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphinic acid
Traditional Name4-cdp-2-C-methyl-D-erythritol
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(O)[C@]1([H])O)[C@@](C)(O)CO
InChI Identifier
InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1
InChI KeyYFAUKWZNPVBCFF-XHIBXCGHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Tetrahydrofuran
  • Tertiary alcohol
  • Heteroaromatic compound
  • Secondary alcohol
  • Polyol
  • Azacycle
  • Oxacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Amine
  • Organic oxide
  • Organooxygen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Primary alcohol
  • Primary amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.8ALOGPS
logP-5.3ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)3.34ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area272.35 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity115.04 m³·mol⁻¹ChemAxon
Polarizability44.23 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+203.85332859911
AllCCS[M+H-H2O]+202.3532859911
AllCCS[M+Na]+205.59632859911
AllCCS[M+NH4]+205.21232859911
AllCCS[M-H]-202.53432859911
AllCCS[M+Na-2H]-203.632859911
AllCCS[M+HCOO]-204.9132859911
DeepCCS[M+H]+190.70730932474
DeepCCS[M-H]-188.76130932474
DeepCCS[M-2H]-222.6530932474
DeepCCS[M+Na]+196.6230932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Positive-QTOFsplash10-03di-0900010000-dd055cf6bd442a4186472015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Positive-QTOFsplash10-03di-2900000000-4e622642413e6ebd84772015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Positive-QTOFsplash10-03di-6900000000-74e9c9a2a9edbdec480f2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Negative-QTOFsplash10-024i-8921880000-a4764a7c92b71559f8022015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Negative-QTOFsplash10-01t9-9873300000-13a6ee53acf7e6b826392015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Negative-QTOFsplash10-0bvl-5900000000-5fb1217b0273b9eb07ed2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Positive-QTOFsplash10-0f79-0002980000-b0c2dd0f91aa67816b822021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Positive-QTOFsplash10-08ou-0689210000-ce579339d5226e7cf7952021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Positive-QTOFsplash10-0gvp-4975000000-183cd21e1b0b0bbffbdd2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Negative-QTOFsplash10-00di-0000090000-641c25f0d0828a8b13d82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Negative-QTOFsplash10-00fr-4211970000-3141df7963d44155286b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Negative-QTOFsplash10-004i-9134000000-c51a8f7c77198cc212bd2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03687
Phenol Explorer Compound IDNot Available
FooDB IDFDB030479
KNApSAcK IDC00007620
Chemspider ID391471
KEGG Compound IDC11435
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound443199
PDB IDNot Available
ChEBI ID16578
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available