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Showing metabocard for 1,3-Dioxane (HMDB0244172)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:21:17 UTC
Update Date2021-09-26 22:51:45 UTC
HMDB IDHMDB0244172
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,3-Dioxane
Description1,3-Dioxane, also known as dihydro-m-dioxin or m-dioxane, belongs to the class of organic compounds known as 1,3-dioxanes. These are organic compounds containing 1,3-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 3. Based on a literature review a significant number of articles have been published on 1,3-Dioxane. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,3-dioxane is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,3-Dioxane 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0244172 (1,3-Dioxane)


  Mrv1652309102123212D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0244172 (1,3-Dioxane)

HMDB0244172
     RDKit          3D
1,3-Dioxane
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.0416   -0.2995    0.0514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5993    1.1017    0.2843 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253    1.3060   -0.3752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5047    0.3540    0.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2622   -0.8435   -0.4400 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0417   -1.1761   -0.6181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9528   -0.2770   -0.6175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4167   -0.7523    1.0075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4689    1.3643    1.3598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3103    1.8318   -0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3114    0.2155    1.2693 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5657    0.6440   -0.0059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2422   -1.2514   -1.7168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958   -2.2174   -0.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
M  END
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3D SDF for HMDB0244172 (1,3-Dioxane)


  Mrv1652309102123212D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244172

> <DATABASE_NAME>
hmdb

> <SMILES>
C1COCOC1

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O2/c1-2-5-4-6-3-1/h1-4H2

> <INCHI_KEY>
VDFVNEFVBPFDSB-UHFFFAOYSA-N

> <FORMULA>
C4H8O2

> <MOLECULAR_WEIGHT>
88.106

> <EXACT_MASS>
88.052429498

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
8.96021854069425

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-dioxane

> <ALOGPS_LOGP>
-0.14

> <JCHEM_LOGP>
0.07610966466666653

> <ALOGPS_LOGS>
0.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9978989376335936

> <JCHEM_POLAR_SURFACE_AREA>
18.46

> <JCHEM_REFRACTIVITY>
21.7619

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.29e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-dioxane

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0244172 (1,3-Dioxane)

HMDB0244172
     RDKit          3D
1,3-Dioxane
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.0416   -0.2995    0.0514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5993    1.1017    0.2843 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253    1.3060   -0.3752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5047    0.3540    0.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2622   -0.8435   -0.4400 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0417   -1.1761   -0.6181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9528   -0.2770   -0.6175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4167   -0.7523    1.0075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4689    1.3643    1.3598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3103    1.8318   -0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3114    0.2155    1.2693 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5657    0.6440   -0.0059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2422   -1.2514   -1.7168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1958   -2.2174   -0.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
M  END
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PDB for HMDB0244172 (1,3-Dioxane)

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0244172 (1,3-Dioxane)

COMPND    HMDB0244172
HETATM    1  C1  UNL     1      -1.042  -0.299   0.051  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.599   1.102   0.284  1.00  0.00           C  
HETATM    3  O1  UNL     1       0.625   1.306  -0.375  1.00  0.00           O  
HETATM    4  C3  UNL     1       1.505   0.354   0.178  1.00  0.00           C  
HETATM    5  O2  UNL     1       1.262  -0.843  -0.440  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.042  -1.176  -0.618  1.00  0.00           C  
HETATM    7  H1  UNL     1      -1.953  -0.277  -0.618  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.417  -0.752   1.007  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.469   1.364   1.360  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.310   1.832  -0.145  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.311   0.215   1.269  1.00  0.00           H  
HETATM   12  H6  UNL     1       2.566   0.644  -0.006  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.242  -1.251  -1.717  1.00  0.00           H  
HETATM   14  H8  UNL     1      -0.196  -2.217  -0.232  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    9   10
CONECT    3    4
CONECT    4    5   11   12
CONECT    5    6
CONECT    6   13   14
END
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SMILES for HMDB0244172 (1,3-Dioxane)

C1COCOC1
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INCHI for HMDB0244172 (1,3-Dioxane)

InChI=1S/C4H8O2/c1-2-5-4-6-3-1/h1-4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,3-DioxacyclohexaneChEBI
1,3-Propanediol formalChEBI
Dihydro-m-dioxinChEBI
m-DioxaneChEBI
Meta-dioxaneChEBI
Trimethylene glycol methylene etherChEBI
Chemical FormulaC4H8O2
Average Molecular Weight88.106
Monoisotopic Molecular Weight88.052429498
IUPAC Name1,3-dioxane
Traditional Name1,3-dioxane
CAS Registry NumberNot Available
SMILES
C1COCOC1
InChI Identifier
InChI=1S/C4H8O2/c1-2-5-4-6-3-1/h1-4H2
InChI KeyVDFVNEFVBPFDSB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dioxanes. These are organic compounds containing 1,3-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 3.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDioxanes
Sub Class1,3-dioxanes
Direct Parent1,3-dioxanes
Alternative Parents
Substituents
  • Meta-dioxane
  • Oxacycle
  • Acetal
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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-0.14ALOGPS
logP0.076ChemAxon
logS0.41ALOGPS
pKa (Strongest Basic)-4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area18.46 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity21.76 m³·mol⁻¹ChemAxon
Polarizability8.96 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+123.70530932474
DeepCCS[M-H]-121.8130932474
DeepCCS[M-2H]-157.25430932474
DeepCCS[M+Na]+131.75730932474
AllCCS[M+H]+117.232859911
AllCCS[M+H-H2O]+111.932859911
AllCCS[M+NH4]+122.132859911
AllCCS[M+Na]+123.532859911
AllCCS[M-H]-119.532859911
AllCCS[M+Na-2H]-123.332859911
AllCCS[M+HCOO]-127.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.2.21 minutes32390414
Predicted by Siyang on May 30, 20228.5481 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.54 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1028.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid324.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid110.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid216.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid74.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid258.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid336.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)175.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid660.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid159.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid786.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid228.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid239.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate510.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA277.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water180.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,3-DioxaneC1COCOC11039.2Standard polar33892256
1,3-DioxaneC1COCOC1689.5Standard non polar33892256
1,3-DioxaneC1COCOC1672.2Semi standard non polar33892256
Spectra
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 ID10018
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link1,3-Dioxane
METLIN IDNot Available
PubChem Compound10450
PDB IDNot Available
ChEBI ID46924
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 ]