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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:58:50 UTC
Update Date2022-03-07 02:56:13 UTC
HMDB IDHMDB0039499
Secondary Accession Numbers
  • HMDB39499
Metabolite Identification
Common Name1,4-Dideoxy-1,4-imino-D-ribitol
Description1,4-Dideoxy-1,4-imino-D-ribitol, also known as 2-hydroxymethyl-pyrrolidine-3,4-diol or DRIB, belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. 1,4-Dideoxy-1,4-imino-D-ribitol has been detected, but not quantified in, fruits and wax apples (Eugenia javanica). This could make 1,4-dideoxy-1,4-imino-D-ribitol a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1,4-Dideoxy-1,4-imino-D-ribitol.
Structure
Data?1563863387
Synonyms
ValueSource
(+)-1,4-Dideoxy-1,4-imino-D-ribitolHMDB
2-(Hydroxymethyl)-(2R,3R,4S)-3,4-pyrrolidinediolHMDB
2-(Hydroxymethyl)-(2R-(2a,3b,4b))-3,4-pyrrolidinediolHMDB
2-(Hydroxymethyl)-[2R-(2a,3b,4b)]-3,4-pyrrolidinediolHMDB
2-HYDROXYMETHYL-pyrrolidine-3,4-diolHMDB
DRIBHMDB
IminoribitolHMDB
IMRHMDB
Chemical FormulaC5H11NO3
Average Molecular Weight133.1457
Monoisotopic Molecular Weight133.073893223
IUPAC Name2-(hydroxymethyl)pyrrolidine-3,4-diol
Traditional Name2-(hydroxymethyl)pyrrolidine-3,4-diol
CAS Registry Number105990-41-8
SMILES
OCC1NCC(O)C1O
InChI Identifier
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2
InChI KeyOQEBIHBLFRADNM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolidines
Sub ClassNot Available
Direct ParentPyrrolidines
Alternative Parents
Substituents
  • Pyrrolidine
  • 1,2-aminoalcohol
  • Secondary alcohol
  • Secondary aliphatic amine
  • Secondary amine
  • Azacycle
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
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
Water Solubility659 g/LALOGPS
logP-1.8ALOGPS
logP-2.3ChemAxon
logS0.69ALOGPS
pKa (Strongest Acidic)13.32ChemAxon
pKa (Strongest Basic)9.36ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area72.72 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.61 m³·mol⁻¹ChemAxon
Polarizability13.03 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+128.23831661259
DarkChem[M-H]-121.66531661259
DeepCCS[M+H]+130.82630932474
DeepCCS[M-H]-128.74730932474
DeepCCS[M-2H]-164.77430932474
DeepCCS[M+Na]+139.49930932474
AllCCS[M+H]+130.532859911
AllCCS[M+H-H2O]+125.932859911
AllCCS[M+NH4]+134.832859911
AllCCS[M+Na]+136.132859911
AllCCS[M-H]-123.732859911
AllCCS[M+Na-2H]-125.832859911
AllCCS[M+HCOO]-128.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,4-Dideoxy-1,4-imino-D-ribitolOCC1NCC(O)C1O3049.2Standard polar33892256
1,4-Dideoxy-1,4-imino-D-ribitolOCC1NCC(O)C1O1315.3Standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitolOCC1NCC(O)C1O1679.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1,4-Dideoxy-1,4-imino-D-ribitol,1TMS,isomer #1C[Si](C)(C)OCC1NCC(O)C1O1496.9Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,1TMS,isomer #2C[Si](C)(C)OC1CNC(CO)C1O1496.8Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,1TMS,isomer #3C[Si](C)(C)OC1C(O)CNC1CO1493.7Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,1TMS,isomer #4C[Si](C)(C)N1CC(O)C(O)C1CO1458.1Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TMS,isomer #1C[Si](C)(C)OCC1NCC(O[Si](C)(C)C)C1O1527.9Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TMS,isomer #2C[Si](C)(C)OCC1NCC(O)C1O[Si](C)(C)C1523.7Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TMS,isomer #3C[Si](C)(C)OCC1C(O)C(O)CN1[Si](C)(C)C1526.1Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TMS,isomer #4C[Si](C)(C)OC1CNC(CO)C1O[Si](C)(C)C1529.3Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TMS,isomer #5C[Si](C)(C)OC1CN([Si](C)(C)C)C(CO)C1O1513.2Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TMS,isomer #6C[Si](C)(C)OC1C(O)CN([Si](C)(C)C)C1CO1519.8Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TMS,isomer #1C[Si](C)(C)OCC1NCC(O[Si](C)(C)C)C1O[Si](C)(C)C1561.1Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TMS,isomer #2C[Si](C)(C)OCC1C(O)C(O[Si](C)(C)C)CN1[Si](C)(C)C1586.1Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TMS,isomer #3C[Si](C)(C)OCC1C(O[Si](C)(C)C)C(O)CN1[Si](C)(C)C1588.2Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TMS,isomer #4C[Si](C)(C)OC1CN([Si](C)(C)C)C(CO)C1O[Si](C)(C)C1559.5Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,4TMS,isomer #1C[Si](C)(C)OCC1C(O[Si](C)(C)C)C(O[Si](C)(C)C)CN1[Si](C)(C)C1650.7Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,4TMS,isomer #1C[Si](C)(C)OCC1C(O[Si](C)(C)C)C(O[Si](C)(C)C)CN1[Si](C)(C)C1697.9Standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1NCC(O)C1O1719.5Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1CNC(CO)C1O1718.2Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC1C(O)CNC1CO1724.6Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)N1CC(O)C(O)C1CO1690.8Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1NCC(O[Si](C)(C)C(C)(C)C)C1O1953.5Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCC1NCC(O)C1O[Si](C)(C)C(C)(C)C1948.3Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OCC1C(O)C(O)CN1[Si](C)(C)C(C)(C)C2002.5Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC1CNC(CO)C1O[Si](C)(C)C(C)(C)C1971.8Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC1CN([Si](C)(C)C(C)(C)C)C(CO)C1O1976.2Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC1C(O)CN([Si](C)(C)C(C)(C)C)C1CO1981.5Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1NCC(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C2202.4Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCC1C(O)C(O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C2255.6Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OCC1C(O[Si](C)(C)C(C)(C)C)C(O)CN1[Si](C)(C)C(C)(C)C2261.7Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC1CN([Si](C)(C)C(C)(C)C)C(CO)C1O[Si](C)(C)C(C)(C)C2245.9Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C2523.9Semi standard non polar33892256
1,4-Dideoxy-1,4-imino-D-ribitol,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C2505.6Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-9300000000-f23c9a4f171e1152f8cd2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol GC-MS (3 TMS) - 70eV, Positivesplash10-0032-4291000000-b3faddd4d0656d1947542017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 10V, Positive-QTOFsplash10-00lr-1900000000-a3fd3276e89e0741b78b2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 20V, Positive-QTOFsplash10-00kb-9700000000-262f43f2a39279208ba92015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 40V, Positive-QTOFsplash10-0002-9000000000-f592217fddd172b3bceb2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 10V, Negative-QTOFsplash10-001i-1900000000-79101bb450a92b55c7072015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 20V, Negative-QTOFsplash10-0w30-5900000000-131d7c9c8faad0c364392015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 40V, Negative-QTOFsplash10-0006-9000000000-a8f9f66c63509a9cc3532015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 10V, Negative-QTOFsplash10-0ue9-0900000000-d7ddef4d09137dda450c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 20V, Negative-QTOFsplash10-0zgi-9500000000-571e3b76b70f4e7e07fd2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 40V, Negative-QTOFsplash10-0a4l-9000000000-cd83a3c53da085536ec72021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 10V, Positive-QTOFsplash10-015a-5900000000-e3cf2bca6b9da0221bb92021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 20V, Positive-QTOFsplash10-0002-9200000000-5d29c2463648aff0184a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Dideoxy-1,4-imino-D-ribitol 40V, Positive-QTOFsplash10-0007-9000000000-f4c4773da7b9c344047c2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019106
KNApSAcK IDC00036384
Chemspider ID1295
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1335
PDB IDNot Available
ChEBI IDNot Available
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 References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .