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Showing metabocard for alpha-Methylene-gamma-butyrolactone (HMDB0246945)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:58:05 UTC
Update Date2021-09-26 22:56:20 UTC
HMDB IDHMDB0246945
Secondary Accession NumbersNone
Metabolite Identification
Common Namealpha-Methylene-gamma-butyrolactone
Descriptionalpha-Methylene-gamma-butyrolactone, also known as α-methylidene-γ-butyrolactone or tulipalin a, belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. Based on a literature review very few articles have been published on alpha-Methylene-gamma-butyrolactone. This compound has been identified in human blood as reported by (PMID: 31557052 ). Alpha-methylene-gamma-butyrolactone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically alpha-Methylene-gamma-butyrolactone 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 HMDB0246945 (alpha-Methylene-gamma-butyrolactone)


  Mrv1533004161514452D          

  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
    0.5678    1.1143    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
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
Download

3D MOL for HMDB0246945 (alpha-Methylene-gamma-butyrolactone)

HMDB0246945
     RDKit          3D
alpha-Methylene-gamma-butyrolactone
 13 13  0  0  0  0  0  0  0  0999 V2000
    1.9386   -0.2690    0.2235 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6793    0.0415   -0.0026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4729   -0.9043   -0.1730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6455    0.0258    0.0173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1762    1.3368   -0.2284 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1874    1.3966   -0.1275 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8868    2.4657   -0.1424 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1976   -1.3168    0.2992 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6760    0.4965    0.3279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4137   -1.3321   -1.1856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3946   -1.6792    0.5943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4824   -0.1899   -0.6675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9805   -0.0716    1.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
M  END
Download

3D SDF for HMDB0246945 (alpha-Methylene-gamma-butyrolactone)


  Mrv1533004161514452D          

  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
    0.5678    1.1143    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
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246945

> <DATABASE_NAME>
hmdb

> <SMILES>
C=C1CCOC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O2/c1-4-2-3-7-5(4)6/h1-3H2

> <INCHI_KEY>
GSLDEZOOOSBFGP-UHFFFAOYSA-N

> <FORMULA>
C5H6O2

> <MOLECULAR_WEIGHT>
98.101

> <EXACT_MASS>
98.036779433

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.421352634592743

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylideneoxolan-2-one

> <ALOGPS_LOGP>
0.39

> <JCHEM_LOGP>
0.8341922883333334

> <ALOGPS_LOGS>
0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.847029159484089

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
24.686

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.13e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tulipalin A

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0246945 (alpha-Methylene-gamma-butyrolactone)

HMDB0246945
     RDKit          3D
alpha-Methylene-gamma-butyrolactone
 13 13  0  0  0  0  0  0  0  0999 V2000
    1.9386   -0.2690    0.2235 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6793    0.0415   -0.0026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4729   -0.9043   -0.1730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6455    0.0258    0.0173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1762    1.3368   -0.2284 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1874    1.3966   -0.1275 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8868    2.4657   -0.1424 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1976   -1.3168    0.2992 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6760    0.4965    0.3279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4137   -1.3321   -1.1856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3946   -1.6792    0.5943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4824   -0.1899   -0.6675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9805   -0.0716    1.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
M  END
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PDB for HMDB0246945 (alpha-Methylene-gamma-butyrolactone)

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   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       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.290  -0.290   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0246945 (alpha-Methylene-gamma-butyrolactone)

COMPND    HMDB0246945
HETATM    1  C1  UNL     1       1.939  -0.269   0.224  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.679   0.042  -0.003  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.473  -0.904  -0.173  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.645   0.026   0.017  1.00  0.00           C  
HETATM    5  O1  UNL     1      -1.176   1.337  -0.228  1.00  0.00           O  
HETATM    6  C5  UNL     1       0.187   1.397  -0.127  1.00  0.00           C  
HETATM    7  O2  UNL     1       0.887   2.466  -0.142  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.198  -1.317   0.299  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.676   0.497   0.328  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.414  -1.332  -1.186  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.395  -1.679   0.594  1.00  0.00           H  
HETATM   12  H5  UNL     1      -2.482  -0.190  -0.667  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.981  -0.072   1.065  1.00  0.00           H  
CONECT    1    2    2    8    9
CONECT    2    3    6
CONECT    3    4   10   11
CONECT    4    5   12   13
CONECT    5    6
CONECT    6    7    7
END
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SMILES for HMDB0246945 (alpha-Methylene-gamma-butyrolactone)

C=C1CCOC1=O
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INCHI for HMDB0246945 (alpha-Methylene-gamma-butyrolactone)

InChI=1S/C5H6O2/c1-4-2-3-7-5(4)6/h1-3H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-Methylenedihydro-2(3H)-furanoneChEBI
alpha-Methylene butyrolactoneChEBI
alpha-Methylidene-gamma-butyrolactoneChEBI
Dihydro-3-methylene-2(3H)-furanoneChEBI
Tulipalin aChEBI
2-MethylenebutanolactoneKegg
a-Methylene butyrolactoneGenerator
Α-methylene butyrolactoneGenerator
a-Methylidene-g-butyrolactoneGenerator
Α-methylidene-γ-butyrolactoneGenerator
a-Methylene-g-butyrolactoneGenerator
Α-methylene-γ-butyrolactoneGenerator
a-Methylene g-butyrolactoneHMDB
Α-methylene γ-butyrolactoneHMDB
alpha-Methylene gamma-butyrolactoneHMDB
alpha-Methylene-gamma-butyrolactoneChEBI
Chemical FormulaC5H6O2
Average Molecular Weight98.101
Monoisotopic Molecular Weight98.036779433
IUPAC Name3-methylideneoxolan-2-one
Traditional Nametulipalin A
CAS Registry NumberNot Available
SMILES
C=C1CCOC1=O
InChI Identifier
InChI=1S/C5H6O2/c1-4-2-3-7-5(4)6/h1-3H2
InChI KeyGSLDEZOOOSBFGP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassLactones
Sub ClassGamma butyrolactones
Direct ParentGamma butyrolactones
Alternative Parents
Substituents
  • Gamma butyrolactone
  • Alpha,beta-unsaturated carboxylic ester
  • Enoate ester
  • Tetrahydrofuran
  • Carboxylic acid ester
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • 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
logP0.39ALOGPS
logP0.83ChemAxon
logS0.06ALOGPS
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.69 m³·mol⁻¹ChemAxon
Polarizability9.42 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]+131.1130932474
DeepCCS[M-H]-128.3530932474
DeepCCS[M-2H]-164.72630932474
DeepCCS[M+Na]+139.42430932474
AllCCS[M+H]+119.132859911
AllCCS[M+H-H2O]+114.132859911
AllCCS[M+NH4]+123.932859911
AllCCS[M+Na]+125.232859911
AllCCS[M-H]-116.932859911
AllCCS[M+Na-2H]-120.032859911
AllCCS[M+HCOO]-123.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
alpha-Methylene-gamma-butyrolactoneC=C1CCOC1=O1660.0Standard polar33892256
alpha-Methylene-gamma-butyrolactoneC=C1CCOC1=O835.9Standard non polar33892256
alpha-Methylene-gamma-butyrolactoneC=C1CCOC1=O1050.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - alpha-Methylene-gamma-butyrolactone GC-MS (Non-derivatized) - 70eV, Positivesplash10-0udj-9000000000-487f83d08065695034c92021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - alpha-Methylene-gamma-butyrolactone 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 - alpha-Methylene-gamma-butyrolactone 10V, Positive-QTOFsplash10-0002-9000000000-c45d8f2f7586116bdfee2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 20V, Positive-QTOFsplash10-0002-9000000000-a8073757d03d8ba3677a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 40V, Positive-QTOFsplash10-0zfr-9000000000-60eeed360fba53f0436e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 10V, Negative-QTOFsplash10-0002-9000000000-aaec60432819fd6b17312016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 20V, Negative-QTOFsplash10-0udj-9000000000-153ff3cfde6b44f6f0a42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 40V, Negative-QTOFsplash10-0udi-9000000000-d97023c0ff6e34caf7862016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 10V, Positive-QTOFsplash10-052b-9000000000-cc2bb18b6b015369905f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 20V, Positive-QTOFsplash10-0zfu-9000000000-8fcfaace5e4a8c70b5df2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 40V, Positive-QTOFsplash10-0udi-9000000000-76bd7b6c1c60870b54192021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 10V, Negative-QTOFsplash10-0002-9000000000-dbbfc6dec07aeb7b66c02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 20V, Negative-QTOFsplash10-0uxs-9000000000-5bc5e4d0490a3ce71e632021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-Methylene-gamma-butyrolactone 40V, Negative-QTOFsplash10-0f6x-9000000000-260134a476cb143d08e22021-10-12Wishart 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 IDC00040580
Chemspider ID61647
KEGG Compound IDC20578
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound68352
PDB IDNot Available
ChEBI ID104120
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1218461
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 ]