Hmdb loader

Showing metabocard for Vinyl butyrate (HMDB0259821)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 22:45:14 UTC
Update Date2021-09-26 23:17:37 UTC
HMDB IDHMDB0259821
Secondary Accession NumbersNone
Metabolite Identification
Common NameVinyl butyrate
DescriptionVinyl butyrate belongs to the class of organic compounds known as fatty acid esters. These are carboxylic ester derivatives of a fatty acid. Based on a literature review a significant number of articles have been published on Vinyl butyrate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Vinyl butyrate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Vinyl butyrate 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0259821 (Vinyl butyrate)


  Mrv1652309122100452D          

  8  7  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
Download

3D MOL for HMDB0259821 (Vinyl butyrate)

HMDB0259821
     RDKit          3D
Vinyl butyrate
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.8071    1.2552    0.0473 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3261    0.5848   -0.9732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9831    0.2990   -1.0957 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3497   -0.8134   -0.6178 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0523   -1.6698   -0.0024 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0973   -1.0932   -0.7648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8390   -0.7608    0.5167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6494    0.7161    0.8367 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1905    1.6301    0.8613 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8629    1.4742    0.1333 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9966    0.2477   -1.7372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2140   -2.1739   -0.9956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5705   -0.5012   -1.5691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9070   -0.9104    0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4831   -1.4252    1.3182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8092    0.8381    1.5379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4441    1.2527   -0.1108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5546    1.0498    1.3555 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
M  END
Download

3D SDF for HMDB0259821 (Vinyl butyrate)


  Mrv1652309122100452D          

  8  7  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259821

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCC(=O)OC=C

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O2/c1-3-5-6(7)8-4-2/h4H,2-3,5H2,1H3

> <INCHI_KEY>
MEGHWIAOTJPCHQ-UHFFFAOYSA-N

> <FORMULA>
C6H10O2

> <MOLECULAR_WEIGHT>
114.144

> <EXACT_MASS>
114.068079562

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.35222865973801

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
ethenyl butanoate

> <ALOGPS_LOGP>
1.84

> <JCHEM_LOGP>
1.5723272536666664

> <ALOGPS_LOGS>
-0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.154636759435345

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
30.332900000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vinyl butyrate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0259821 (Vinyl butyrate)

HMDB0259821
     RDKit          3D
Vinyl butyrate
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.8071    1.2552    0.0473 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3261    0.5848   -0.9732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9831    0.2990   -1.0957 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3497   -0.8134   -0.6178 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0523   -1.6698   -0.0024 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0973   -1.0932   -0.7648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8390   -0.7608    0.5167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6494    0.7161    0.8367 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1905    1.6301    0.8613 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8629    1.4742    0.1333 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9966    0.2477   -1.7372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2140   -2.1739   -0.9956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5705   -0.5012   -1.5691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9070   -0.9104    0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4831   -1.4252    1.3182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8092    0.8381    1.5379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4441    1.2527   -0.1108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5546    1.0498    1.3555 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
M  END
Download

PDB for HMDB0259821 (Vinyl butyrate)

HEADER    PROTEIN                                 12-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-21         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       8.621   3.437   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
Download

3D PDB for HMDB0259821 (Vinyl butyrate)

COMPND    HMDB0259821
HETATM    1  C1  UNL     1       2.807   1.255   0.047  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.326   0.585  -0.973  1.00  0.00           C  
HETATM    3  O1  UNL     1       0.983   0.299  -1.096  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.350  -0.813  -0.618  1.00  0.00           C  
HETATM    5  O2  UNL     1       1.052  -1.670  -0.002  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.097  -1.093  -0.765  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.839  -0.761   0.517  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.649   0.716   0.837  1.00  0.00           C  
HETATM    9  H1  UNL     1       2.191   1.630   0.861  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.863   1.474   0.133  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.997   0.248  -1.737  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.214  -2.174  -0.996  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.570  -0.501  -1.569  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.907  -0.910   0.304  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.483  -1.425   1.318  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.809   0.838   1.538  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.444   1.253  -0.111  1.00  0.00           H  
HETATM   18  H10 UNL     1      -2.555   1.050   1.356  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4
CONECT    4    5    5    6
CONECT    6    7   12   13
CONECT    7    8   14   15
CONECT    8   16   17   18
END
Download

SMILES for HMDB0259821 (Vinyl butyrate)

CCCC(=O)OC=C
Download

INCHI for HMDB0259821 (Vinyl butyrate)

InChI=1S/C6H10O2/c1-3-5-6(7)8-4-2/h4H,2-3,5H2,1H3
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Vinyl butyric acidGenerator
Ethenyl butanoic acidHMDB
Butanoic acid, etheyl esterHMDB
Vinyl butanoateHMDB
Chemical FormulaC6H10O2
Average Molecular Weight114.144
Monoisotopic Molecular Weight114.068079562
IUPAC Nameethenyl butanoate
Traditional Namevinyl butyrate
CAS Registry NumberNot Available
SMILES
CCCC(=O)OC=C
InChI Identifier
InChI=1S/C6H10O2/c1-3-5-6(7)8-4-2/h4H,2-3,5H2,1H3
InChI KeyMEGHWIAOTJPCHQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty acid esters. These are carboxylic ester derivatives of a fatty acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acid esters
Direct ParentFatty acid esters
Alternative Parents
Substituents
  • Fatty acid ester
  • Enol ester
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
logP1.84ALOGPS
logP1.57ChemAxon
logS-0.9ALOGPS
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.33 m³·mol⁻¹ChemAxon
Polarizability12.35 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
AllCCS[M+H]+129.1332859911
AllCCS[M+H-H2O]+124.86432859911
AllCCS[M+Na]+134.25732859911
AllCCS[M+NH4]+133.10932859911
AllCCS[M-H]-128.11732859911
AllCCS[M+Na-2H]-131.40832859911
AllCCS[M+HCOO]-135.05632859911
DeepCCS[M+H]+123.40230932474
DeepCCS[M-H]-120.95730932474
DeepCCS[M-2H]-157.1430932474
DeepCCS[M+Na]+131.59930932474

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. Predicted by Afia on May 17, 2022.4.15 minutes32390414
Predicted by Siyang on May 30, 202214.0295 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.95 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1769.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid504.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid189.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid349.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid260.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid473.7 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 Acid645.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)166.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1135.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid401.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1169.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid346.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid393.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate542.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA501.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water82.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Vinyl butyrateCCCC(=O)OC=C1051.6Standard polar33892256
Vinyl butyrateCCCC(=O)OC=C783.8Standard non polar33892256
Vinyl butyrateCCCC(=O)OC=C813.5Semi 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 ID28987
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound31247
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. 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 ]