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Showing metabocard for 2,4-Dimethyl-1,3-dioxolane (HMDB0032230)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:48:37 UTC
Update Date2022-03-07 02:53:17 UTC
HMDB IDHMDB0032230
Secondary Accession Numbers
  • HMDB32230
Metabolite Identification
Common Name2,4-Dimethyl-1,3-dioxolane
Description2,4-Dimethyl-1,3-dioxolane belongs to the class of organic compounds known as 1,3-dioxolanes. These are organic compounds containing 1,3-dioxolane, an aliphatic five-member ring with two oxygen atoms in ring positions 1 and 3. Based on a literature review very few articles have been published on 2,4-Dimethyl-1,3-dioxolane.
Structure
Data?1563862235
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)


  Mrv0541 05061306252D          

  7  7  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)

HMDB0032230
     RDKit          3D
2,4-Dimethyl-1,3-dioxolane
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.2749   -0.0613    0.4972 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -0.4787    0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5084    0.1689   -1.2751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8854   -0.0698   -1.2239 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1497    0.3846    0.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4937   -0.0998    0.5766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1113   -0.0693    0.8761 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0199   -0.8754    0.2651 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6417    0.8547    0.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3493    0.0674    1.6101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556   -1.5887   -0.1381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9842   -0.3060   -2.1301 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6259    1.2584   -1.2058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1578    1.5091   -0.0089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3445   -0.4817    1.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2141    0.7311    0.5035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8167   -0.9436   -0.0844 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
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  6 17  1  0
M  END
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3D SDF for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)


  Mrv0541 05061306252D          

  7  7  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032230

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1COC(C)O1

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O2/c1-4-3-6-5(2)7-4/h4-5H,3H2,1-2H3

> <INCHI_KEY>
ROSFUFIOLRQOON-UHFFFAOYSA-N

> <FORMULA>
C5H10O2

> <MOLECULAR_WEIGHT>
102.1317

> <EXACT_MASS>
102.068079564

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
11.137642789234782

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,4-dimethyl-1,3-dioxolane

> <ALOGPS_LOGP>
0.44

> <JCHEM_LOGP>
0.6622578339999998

> <ALOGPS_LOGS>
0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.0408740851615805

> <JCHEM_POLAR_SURFACE_AREA>
18.46

> <JCHEM_REFRACTIVITY>
26.1576

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4-dimethyl-1,3-dioxolane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)

HMDB0032230
     RDKit          3D
2,4-Dimethyl-1,3-dioxolane
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.2749   -0.0613    0.4972 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -0.4787    0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5084    0.1689   -1.2751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8854   -0.0698   -1.2239 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1497    0.3846    0.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4937   -0.0998    0.5766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1113   -0.0693    0.8761 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0199   -0.8754    0.2651 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6417    0.8547    0.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3493    0.0674    1.6101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556   -1.5887   -0.1381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9842   -0.3060   -2.1301 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6259    1.2584   -1.2058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1578    1.5091   -0.0089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3445   -0.4817    1.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2141    0.7311    0.5035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8167   -0.9436   -0.0844 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
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  6 17  1  0
M  END
Download

PDB for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    5                                                            
CONECT    3    4    6                                                       
CONECT    4    1    3    7                                                  
CONECT    5    2    6    7                                                  
CONECT    6    3    5                                                       
CONECT    7    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)

COMPND    HMDB0032230
HETATM    1  C1  UNL     1       2.275  -0.061   0.497  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.913  -0.479   0.056  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.508   0.169  -1.275  1.00  0.00           C  
HETATM    4  O1  UNL     1      -0.885  -0.070  -1.224  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.150   0.385   0.081  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.494  -0.100   0.577  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.111  -0.069   0.876  1.00  0.00           O  
HETATM    8  H1  UNL     1       3.020  -0.875   0.265  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.642   0.855   0.001  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.349   0.067   1.610  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.856  -1.589  -0.138  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.984  -0.306  -2.130  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.626   1.258  -1.206  1.00  0.00           H  
HETATM   14  H7  UNL     1      -1.158   1.509  -0.009  1.00  0.00           H  
HETATM   15  H8  UNL     1      -2.344  -0.482   1.599  1.00  0.00           H  
HETATM   16  H9  UNL     1      -3.214   0.731   0.504  1.00  0.00           H  
HETATM   17  H10 UNL     1      -2.817  -0.944  -0.084  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    7   11
CONECT    3    4   12   13
CONECT    4    5
CONECT    5    6    7   14
CONECT    6   15   16   17
END
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SMILES for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)

CC1COC(C)O1
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INCHI for HMDB0032230 (2,4-Dimethyl-1,3-dioxolane)

InChI=1S/C5H10O2/c1-4-3-6-5(2)7-4/h4-5H,3H2,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,3-Dioxolane, 2,4-dimethyl, cisHMDB
1,3-Dioxolane, 2,4-dimethyl, transHMDB
Chemical FormulaC5H10O2
Average Molecular Weight102.1317
Monoisotopic Molecular Weight102.068079564
IUPAC Name2,4-dimethyl-1,3-dioxolane
Traditional Name2,4-dimethyl-1,3-dioxolane
CAS Registry Number3390-12-3
SMILES
CC1COC(C)O1
InChI Identifier
InChI=1S/C5H10O2/c1-4-3-6-5(2)7-4/h4-5H,3H2,1-2H3
InChI KeyROSFUFIOLRQOON-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dioxolanes. These are organic compounds containing 1,3-dioxolane, an aliphatic five-member ring with two oxygen atoms in ring positions 1 and 3.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDioxolanes
Sub Class1,3-dioxolanes
Direct Parent1,3-dioxolanes
Alternative Parents
Substituents
  • Meta-dioxolane
  • Oxacycle
  • Acetal
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
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
Water Solubility127 g/LALOGPS
logP0.44ALOGPS
logP0.66ChemAxon
logS0.09ALOGPS
pKa (Strongest Basic)-4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area18.46 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.16 m³·mol⁻¹ChemAxon
Polarizability11.14 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
DarkChem[M+H]+120.87131661259
DarkChem[M-H]-115.9931661259
DeepCCS[M+H]+129.39230932474
DeepCCS[M-H]-127.49730932474
DeepCCS[M-2H]-163.03230932474
DeepCCS[M+Na]+137.57430932474
AllCCS[M+H]+122.332859911
AllCCS[M+H-H2O]+117.332859911
AllCCS[M+NH4]+126.932859911
AllCCS[M+Na]+128.232859911
AllCCS[M-H]-122.832859911
AllCCS[M+Na-2H]-126.132859911
AllCCS[M+HCOO]-129.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,4-Dimethyl-1,3-dioxolaneCC1COC(C)O1940.8Standard polar33892256
2,4-Dimethyl-1,3-dioxolaneCC1COC(C)O1661.3Standard non polar33892256
2,4-Dimethyl-1,3-dioxolaneCC1COC(C)O1670.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2,4-Dimethyl-1,3-dioxolane GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a6u-9000000000-5b33a09d73b181061fe92017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 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 - 2,4-Dimethyl-1,3-dioxolane 10V, Negative-QTOFsplash10-0udi-0900000000-f852035ab46960b331332016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 20V, Negative-QTOFsplash10-0udi-5900000000-5f9f4c1755c9ce74140f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 40V, Negative-QTOFsplash10-0006-9000000000-b7a14ac9ee5b1f0b19be2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 10V, Negative-QTOFsplash10-0a4i-9100000000-44a3fc028392379af6382021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 20V, Negative-QTOFsplash10-052f-9100000000-bf2486aae0ac67b698b42021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 40V, Negative-QTOFsplash10-052f-9000000000-8c507ce40d34bbfa52432021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 10V, Positive-QTOFsplash10-0udi-1900000000-8878abb8d9e9896763fa2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 20V, Positive-QTOFsplash10-0udi-5900000000-1df670fc79ad4e46382f2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 40V, Positive-QTOFsplash10-056r-9000000000-661e2de0474bfe347d4d2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 10V, Positive-QTOFsplash10-0pbd-9100000000-8aa67c37ae81c9ec6a7d2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 20V, Positive-QTOFsplash10-0006-9000000000-00762264cf8ad5195d3b2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,4-Dimethyl-1,3-dioxolane 40V, Positive-QTOFsplash10-0006-9000000000-3bf4cbc7f58dfaef4df42021-09-24Wishart 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 IDFDB009310
KNApSAcK IDNot Available
Chemspider ID93045
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound102993
PDB IDNot Available
ChEBI ID173351
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. (). EAFUS: Everything Added to Food in the United States.. .