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Showing metabocard for xi-3-Methyl-3-buten-2-ol (HMDB0039779)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:19:09 UTC
Update Date2023-02-21 17:27:07 UTC
HMDB IDHMDB0039779
Secondary Accession Numbers
  • HMDB39779
Metabolite Identification
Common Namexi-3-Methyl-3-buten-2-ol
Descriptionxi-3-Methyl-3-buten-2-ol belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl). xi-3-Methyl-3-buten-2-ol has been detected, but not quantified in, several different foods, such as breakfast cereal, cereals and cereal products, citrus, and fruits. This could make XI-3-methyl-3-buten-2-ol a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on xi-3-Methyl-3-buten-2-ol.
Structure
Data?1677000427
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)


  Mrv0541 05061311242D          

  6  5  0  0  0  0            999 V2000
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    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
  4  1  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)

HMDB0039779
     RDKit          3D
xi-3-Methyl-3-buten-2-ol
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.2841    1.1864   -0.7644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6816    0.2067   -0.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3221   -1.1393   -0.0956 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297    0.3472    0.5501 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5940   -0.6140   -0.0996 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0964    1.6516    0.5554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2334    1.0577   -1.2547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8138    2.1687   -0.7940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5385   -1.8806   -0.3028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1432   -1.2192   -0.8403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7294   -1.2256    0.9554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5498    0.0386    1.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5556   -0.0845   -0.3613 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8354   -1.4728    0.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1912   -1.0143   -1.0713 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2940    1.9935    1.4730 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  1  7  1  0
  1  8  1  0
  3  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
M  END
Download

3D SDF for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)


  Mrv0541 05061311242D          

  6  5  0  0  0  0            999 V2000
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    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
  4  1  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0039779

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C(C)=C

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O/c1-4(2)5(3)6/h5-6H,1H2,2-3H3

> <INCHI_KEY>
JEYLKNVLTAPJAF-UHFFFAOYSA-N

> <FORMULA>
C5H10O

> <MOLECULAR_WEIGHT>
86.1323

> <EXACT_MASS>
86.073164942

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.158105507138796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylbut-3-en-2-ol

> <ALOGPS_LOGP>
0.96

> <JCHEM_LOGP>
0.8726090510000001

> <ALOGPS_LOGS>
0.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.45289351943246

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7259043746002414

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
26.1248

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.17e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-buten-2-ol, 3-methyl-

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)

HMDB0039779
     RDKit          3D
xi-3-Methyl-3-buten-2-ol
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.2841    1.1864   -0.7644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6816    0.2067   -0.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3221   -1.1393   -0.0956 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297    0.3472    0.5501 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5940   -0.6140   -0.0996 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0964    1.6516    0.5554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2334    1.0577   -1.2547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8138    2.1687   -0.7940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5385   -1.8806   -0.3028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1432   -1.2192   -0.8403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7294   -1.2256    0.9554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5498    0.0386    1.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5556   -0.0845   -0.3613 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8354   -1.4728    0.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1912   -1.0143   -1.0713 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2940    1.9935    1.4730 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  1  7  1  0
  1  8  1  0
  3  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
M  END
Download

PDB for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)

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       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    4                                                            
CONECT    3    5                                                            
CONECT    4    1    2    5                                                  
CONECT    5    3    4    6                                                  
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)

COMPND    HMDB0039779
HETATM    1  C1  UNL     1      -1.284   1.186  -0.764  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.682   0.207  -0.138  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.322  -1.139  -0.096  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.630   0.347   0.550  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.594  -0.614  -0.100  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.096   1.652   0.555  1.00  0.00           O  
HETATM    7  H1  UNL     1      -2.233   1.058  -1.255  1.00  0.00           H  
HETATM    8  H2  UNL     1      -0.814   2.169  -0.794  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.538  -1.881  -0.303  1.00  0.00           H  
HETATM   10  H4  UNL     1      -2.143  -1.219  -0.840  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.729  -1.226   0.955  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.550   0.039   1.629  1.00  0.00           H  
HETATM   13  H7  UNL     1       2.556  -0.084  -0.361  1.00  0.00           H  
HETATM   14  H8  UNL     1       1.835  -1.473   0.559  1.00  0.00           H  
HETATM   15  H9  UNL     1       1.191  -1.014  -1.071  1.00  0.00           H  
HETATM   16  H10 UNL     1       1.294   1.994   1.473  1.00  0.00           H  
CONECT    1    2    2    7    8
CONECT    2    3    4
CONECT    3    9   10   11
CONECT    4    5    6   12
CONECT    5   13   14   15
CONECT    6   16
END
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SMILES for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)

CC(O)C(C)=C
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INCHI for HMDB0039779 (xi-3-Methyl-3-buten-2-ol)

InChI=1S/C5H10O/c1-4(2)5(3)6/h5-6H,1H2,2-3H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H10O
Average Molecular Weight86.1323
Monoisotopic Molecular Weight86.073164942
IUPAC Name3-methylbut-3-en-2-ol
Traditional Name3-buten-2-ol, 3-methyl-
CAS Registry NumberNot Available
SMILES
CC(O)C(C)=C
InChI Identifier
InChI=1S/C5H10O/c1-4(2)5(3)6/h5-6H,1H2,2-3H3
InChI KeyJEYLKNVLTAPJAF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentSecondary alcohols
Alternative Parents
Substituents
  • Secondary alcohol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological 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 Solubility117 g/LALOGPS
logP0.96ALOGPS
logP0.87ChemAxon
logS0.13ALOGPS
pKa (Strongest Acidic)17.45ChemAxon
pKa (Strongest Basic)-1.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity26.12 m³·mol⁻¹ChemAxon
Polarizability10.16 ųChemAxon
Number of Rings0ChemAxon
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]+117.25731661259
DarkChem[M-H]-110.87531661259
DeepCCS[M+H]+122.66130932474
DeepCCS[M-H]-120.60530932474
DeepCCS[M-2H]-156.46230932474
DeepCCS[M+Na]+130.91430932474
AllCCS[M+H]+124.532859911
AllCCS[M+H-H2O]+120.132859911
AllCCS[M+NH4]+128.632859911
AllCCS[M+Na]+129.832859911
AllCCS[M-H]-127.132859911
AllCCS[M+Na-2H]-131.832859911
AllCCS[M+HCOO]-137.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
xi-3-Methyl-3-buten-2-olCC(O)C(C)=C1057.7Standard polar33892256
xi-3-Methyl-3-buten-2-olCC(O)C(C)=C663.0Standard non polar33892256
xi-3-Methyl-3-buten-2-olCC(O)C(C)=C659.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
xi-3-Methyl-3-buten-2-ol,1TMS,isomer #1C=C(C)C(C)O[Si](C)(C)C814.3Semi standard non polar33892256
xi-3-Methyl-3-buten-2-ol,1TBDMS,isomer #1C=C(C)C(C)O[Si](C)(C)C(C)(C)C1023.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - xi-3-Methyl-3-buten-2-ol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-a37d86d9ce4dae6f2cf02017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - xi-3-Methyl-3-buten-2-ol GC-MS (1 TMS) - 70eV, Positivesplash10-0096-9300000000-8d7064fc0f22523081052017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - xi-3-Methyl-3-buten-2-ol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - xi-3-Methyl-3-buten-2-ol 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 - xi-3-Methyl-3-buten-2-ol 10V, Positive-QTOFsplash10-014r-9000000000-f3dbd084e0ae70c9a3bd2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 20V, Positive-QTOFsplash10-014r-9000000000-970663e0b18aad06b06e2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 40V, Positive-QTOFsplash10-0gbc-9000000000-c800bac151c2673a88702016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 10V, Negative-QTOFsplash10-000i-9000000000-fdae2c85486d48463a0c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 20V, Negative-QTOFsplash10-000i-9000000000-b35546bc3dbb9304601f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 40V, Negative-QTOFsplash10-014i-9000000000-764539f4a9e205ed6e912016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 10V, Negative-QTOFsplash10-000i-9000000000-2091e44a102d8284a8132021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 20V, Negative-QTOFsplash10-000i-9000000000-bafbb95f64af9acf8ad52021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 40V, Negative-QTOFsplash10-00ku-9000000000-1c271fcf94b7a65537942021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 10V, Positive-QTOFsplash10-014i-9000000000-8ba63441b0323db747ec2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 20V, Positive-QTOFsplash10-014l-9000000000-4457f76d25f89672810a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - xi-3-Methyl-3-buten-2-ol 40V, Positive-QTOFsplash10-0006-9000000000-7799f9afa159c933b3a82021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX 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 IDFDB019429
KNApSAcK IDNot Available
Chemspider ID59707
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound66329
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.. .