Hmdb loader
Survey
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:12:15 UTC
Update Date2021-10-01 18:49:14 UTC
HMDB IDHMDB0245099
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Deoxy-D-ribose
Description2-deoxypentose belongs to the class of organic compounds known as beta-hydroxy aldehydes. These are organic compounds containing an aldehyde substituted with a hydroxy group on the second carbon atom. Based on a literature review very few articles have been published on 2-deoxypentose. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-deoxy-d-ribose is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Deoxy-D-ribose is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
3,4,5-TrihydroxypentanalChEBI
DeoxyriboseMetaCyc, MeSH
2-DeoxyriboseMetaCyc, MeSH
2-Deoxy-D-riboseMetaCyc
2 DeoxyriboseMeSH
Chemical FormulaC5H10O4
Average Molecular Weight134.131
Monoisotopic Molecular Weight134.057908802
IUPAC Name3,4,5-trihydroxypentanal
Traditional Name3,4,5-trihydroxypentanal
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)CC=O
InChI Identifier
InChI=1S/C5H10O4/c6-2-1-4(8)5(9)3-7/h2,4-5,7-9H,1,3H2
InChI KeyASJSAQIRZKANQN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta-hydroxy aldehydes. These are organic compounds containing an aldehyde substituted with a hydroxy group on the second carbon atom.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentBeta-hydroxy aldehydes
Alternative Parents
Substituents
  • Beta-hydroxy aldehyde
  • Alpha-hydrogen aldehyde
  • Secondary alcohol
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot 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-1.9ALOGPS
logP-2.2ChemAxon
logS0.72ALOGPS
pKa (Strongest Acidic)13.19ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.04 m³·mol⁻¹ChemAxon
Polarizability12.62 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+126.5530932474
DeepCCS[M-H]-123.94830932474
DeepCCS[M-2H]-160.43530932474
DeepCCS[M+Na]+135.11830932474
AllCCS[M+H]+132.732859911
AllCCS[M+H-H2O]+128.632859911
AllCCS[M+NH4]+136.532859911
AllCCS[M+Na]+137.632859911
AllCCS[M-H]-126.032859911
AllCCS[M+Na-2H]-128.632859911
AllCCS[M+HCOO]-131.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Deoxy-D-riboseOCC(O)C(O)CC=O2690.5Standard polar33892256
2-Deoxy-D-riboseOCC(O)C(O)CC=O1215.7Standard non polar33892256
2-Deoxy-D-riboseOCC(O)C(O)CC=O1351.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Deoxy-D-ribose,4TMS,isomer #1C[Si](C)(C)OC=CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O[Si](C)(C)C1627.9Semi standard non polar33892256
2-Deoxy-D-ribose,4TMS,isomer #1C[Si](C)(C)OC=CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O[Si](C)(C)C1597.3Standard non polar33892256
2-Deoxy-D-ribose,4TMS,isomer #1C[Si](C)(C)OC=CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O[Si](C)(C)C1559.1Standard polar33892256
2-Deoxy-D-ribose,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2442.1Semi standard non polar33892256
2-Deoxy-D-ribose,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2354.3Standard non polar33892256
2-Deoxy-D-ribose,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2023.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (Non-derivatized) - 70eV, Positivesplash10-0229-9100000000-5f8fe6400a4de18a43be2018-04-09Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,4,5-trihydroxypentanal GC-MS (TBDMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 10V, Positive-QTOFsplash10-00kr-2900000000-7212141e75dc5de8abb72018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 20V, Positive-QTOFsplash10-0005-9200000000-6a5c150bef435788752e2018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 40V, Positive-QTOFsplash10-052e-9000000000-31a09e36b22561688faf2018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 10V, Negative-QTOFsplash10-001i-3900000000-625c983cf45fad5e70742018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 20V, Negative-QTOFsplash10-0006-9300000000-d8aff4708d60e03edd1e2018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 40V, Negative-QTOFsplash10-0006-9000000000-e7e5ef9e90be1c01e1302018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 10V, Positive-QTOFsplash10-00re-9100000000-74b5bed30f625344268e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 20V, Positive-QTOFsplash10-0005-9000000000-5892767696756a22ae462021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 40V, Positive-QTOFsplash10-0007-9000000000-0489ca73c910ac07f36e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 10V, Negative-QTOFsplash10-05ac-9400000000-ae2841d840c9c0fd74f22021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 20V, Negative-QTOFsplash10-052f-9000000000-f1f804aad64019dd8d532021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribose 40V, Negative-QTOFsplash10-0006-9000000000-d16d81942f2c6df759ea2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10330
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPentose
METLIN IDNot Available
PubChem Compound10786
PDB IDNot Available
ChEBI ID131350
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Only showing the first 10 proteins. There are 35 proteins in total.

Enzymes

General function:
Involved in catalytic activity
Specific function:
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate (By similarity).
Gene Name:
DERA
Uniprot ID:
Q9Y315
Molecular weight:
35230.395
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
Catalyzes the conversion of the nucleoside breakdown products ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. May also catalyze the interconversion of glucose-1-phosphate and glucose-6-phosphate. Has low glucose 1,6-bisphosphate synthase activity.
Gene Name:
PGM2
Uniprot ID:
Q96G03
Molecular weight:
68282.765
General function:
Not Available
Specific function:
Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases (By similarity).
Gene Name:
DNPH1
Uniprot ID:
O43598
Molecular weight:
19108.255
General function:
Not Available
Specific function:
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
Gene Name:
DEOC1
Uniprot ID:
Q6A8F1
Molecular weight:
22616.3
General function:
Not Available
Specific function:
Phosphotransfer between the C1 and C5 carbon atoms of pentose.
Gene Name:
DEOB
Uniprot ID:
Q1JHB7
Molecular weight:
44209.21
General function:
Not Available
Specific function:
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
Gene Name:
DEOC
Uniprot ID:
C0MG52
Molecular weight:
22975.995
General function:
Not Available
Specific function:
Phosphotransfer between the C1 and C5 carbon atoms of pentose.
Gene Name:
DEOB
Uniprot ID:
Q5PK21
Molecular weight:
44303.55
General function:
Not Available
Specific function:
Phosphotransfer between the C1 and C5 carbon atoms of pentose.
Gene Name:
DEOB
Uniprot ID:
A1AJV0
Molecular weight:
44392.64
General function:
Not Available
Specific function:
Phosphotransfer between the C1 and C5 carbon atoms of pentose.
Gene Name:
DEOB
Uniprot ID:
Q1J736
Molecular weight:
44223.23
General function:
Not Available
Specific function:
Phosphotransfer between the C1 and C5 carbon atoms of pentose.
Gene Name:
DEOB1
Uniprot ID:
Q8CMH6
Molecular weight:
44201.18

Only showing the first 10 proteins. There are 35 proteins in total.