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Showing metabocard for delta-Valerolactone (HMDB0250981)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 08:08:33 UTC
Update Date2021-09-26 23:02:44 UTC
HMDB IDHMDB0250981
Secondary Accession NumbersNone
Metabolite Identification
Common Namedelta-Valerolactone
Description5-valerolactone belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. 5-valerolactone is an extremely weak basic (essentially neutral) compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Delta-valerolactone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically delta-Valerolactone 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 HMDB0250981 (delta-Valerolactone)


  Mrv1533004241508262D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0250981 (delta-Valerolactone)

HMDB0250981
     RDKit          3D
delta-Valerolactone
 15 15  0  0  0  0  0  0  0  0999 V2000
   -0.5217    2.6147   -0.8586 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1238    1.5902   -0.2434 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0327    0.6918    0.5176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9778   -0.6645   -0.1499 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4349   -1.0740   -0.3998 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4543   -0.1440    0.2084 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2244    1.2047   -0.2232 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5588    0.5575    1.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0405    1.0808    0.6272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5141   -1.3835    0.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5665   -0.5696   -1.1063 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6735   -1.2023   -1.4874 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6065   -2.0757    0.0535 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4428   -0.4235   -0.2450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4996   -0.2028    1.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
M  END
Download

3D SDF for HMDB0250981 (delta-Valerolactone)


  Mrv1533004241508262D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250981

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCCCO1

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O2/c6-5-3-1-2-4-7-5/h1-4H2

> <INCHI_KEY>
OZJPLYNZGCXSJM-UHFFFAOYSA-N

> <FORMULA>
C5H8O2

> <MOLECULAR_WEIGHT>
100.117

> <EXACT_MASS>
100.052429498

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.13461628715531

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oxan-2-one

> <ALOGPS_LOGP>
0.31

> <JCHEM_LOGP>
0.5941199706666667

> <ALOGPS_LOGS>
-0.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.032743010701426

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
24.9091

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.54e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
delta-valerolactone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0250981 (delta-Valerolactone)

HMDB0250981
     RDKit          3D
delta-Valerolactone
 15 15  0  0  0  0  0  0  0  0999 V2000
   -0.5217    2.6147   -0.8586 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1238    1.5902   -0.2434 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0327    0.6918    0.5176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9778   -0.6645   -0.1499 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4349   -1.0740   -0.3998 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4543   -0.1440    0.2084 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2244    1.2047   -0.2232 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5588    0.5575    1.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0405    1.0808    0.6272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5141   -1.3835    0.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5665   -0.5696   -1.1063 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6735   -1.2023   -1.4874 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6065   -2.0757    0.0535 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4428   -0.4235   -0.2450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4996   -0.2028    1.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
M  END
Download

PDB for HMDB0250981 (delta-Valerolactone)

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0250981 (delta-Valerolactone)

COMPND    HMDB0250981
HETATM    1  O1  UNL     1      -0.522   2.615  -0.859  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.124   1.590  -0.243  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.033   0.692   0.518  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.978  -0.664  -0.150  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.435  -1.074  -0.400  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.454  -0.144   0.208  1.00  0.00           C  
HETATM    7  O2  UNL     1       1.224   1.205  -0.223  1.00  0.00           O  
HETATM    8  H1  UNL     1      -0.559   0.558   1.527  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.041   1.081   0.627  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.514  -1.384   0.480  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.566  -0.570  -1.106  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.673  -1.202  -1.487  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.607  -2.076   0.053  1.00  0.00           H  
HETATM   14  H7  UNL     1       2.443  -0.423  -0.245  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.500  -0.203   1.300  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    8    9
CONECT    4    5   10   11
CONECT    5    6   12   13
CONECT    6    7   14   15
END
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SMILES for HMDB0250981 (delta-Valerolactone)

O=C1CCCCO1
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INCHI for HMDB0250981 (delta-Valerolactone)

InChI=1S/C5H8O2/c6-5-3-1-2-4-7-5/h1-4H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
delta-ValerolactoneChEBI
gamma-ValerolactoneKegg
Δ-valerolactoneGenerator
g-ValerolactoneGenerator
Γ-valerolactoneGenerator
delta-ValerothiolactoneMeSH
Chemical FormulaC5H8O2
Average Molecular Weight100.117
Monoisotopic Molecular Weight100.052429498
IUPAC Nameoxan-2-one
Traditional Namedelta-valerolactone
CAS Registry NumberNot Available
SMILES
O=C1CCCCO1
InChI Identifier
InChI=1S/C5H8O2/c6-5-3-1-2-4-7-5/h1-4H2
InChI KeyOZJPLYNZGCXSJM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassLactones
Sub ClassDelta valerolactones
Direct ParentDelta valerolactones
Alternative Parents
Substituents
  • Delta_valerolactone
  • Delta valerolactone
  • Oxane
  • 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 location
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
logP0.31ALOGPS
logP0.59ChemAxon
logS-0.02ALOGPS
pKa (Strongest Basic)-7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.91 m³·mol⁻¹ChemAxon
Polarizability10.13 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]+126.59330932474
DeepCCS[M-H]-124.52530932474
DeepCCS[M-2H]-160.08630932474
DeepCCS[M+Na]+134.8330932474
AllCCS[M+H]+120.332859911
AllCCS[M+H-H2O]+115.232859911
AllCCS[M+NH4]+125.132859911
AllCCS[M+Na]+126.532859911
AllCCS[M-H]-121.032859911
AllCCS[M+Na-2H]-124.032859911
AllCCS[M+HCOO]-127.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
delta-ValerolactoneO=C1CCCCO11774.6Standard polar33892256
delta-ValerolactoneO=C1CCCCO1920.0Standard non polar33892256
delta-ValerolactoneO=C1CCCCO1990.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - delta-Valerolactone GC-MS (Non-derivatized) - 70eV, Positivesplash10-054o-9000000000-34336070dde59755b5d52021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - delta-Valerolactone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 10V, Positive-QTOFsplash10-0a4i-9000000000-5e003a36aac35e9de7f82021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 35V, Positive-QTOFsplash10-0a4i-9100000000-32b1c226d267d629cdc92021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 20V, Positive-QTOFsplash10-0a4i-9000000000-78ad8ce8c84e9f0248b92021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 40V, Positive-QTOFsplash10-0006-9000000000-6892bb7af52f0f75e5872021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 35V, Positive-QTOFsplash10-0a4i-9100000000-f0fa58c72c0169617ccb2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 35V, Positive-QTOFsplash10-0a4i-9200000000-f816f512be6d40cc0c992021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 35V, Positive-QTOFsplash10-0udi-6900000000-49e1b4a1bcc6a11afe3d2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - delta-Valerolactone 35V, Positive-QTOFsplash10-0udi-6900000000-59112f305c151baffc662021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 10V, Positive-QTOFsplash10-0udi-6900000000-0f249f9b13b315a624262016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 20V, Positive-QTOFsplash10-0zfr-9300000000-99efd1fb74bf8c8d06232016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 40V, Positive-QTOFsplash10-052f-9000000000-632e27a167ffd29da2e62016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 10V, Negative-QTOFsplash10-0002-9000000000-6ac9803189ee1286d4452016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 20V, Negative-QTOFsplash10-0002-9000000000-4fd5f1109cdf83bb602b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 40V, Negative-QTOFsplash10-0007-9000000000-6201244c356de7246f882016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 10V, Positive-QTOFsplash10-0udi-7900000000-d7f745bab582ce8d8dae2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 20V, Positive-QTOFsplash10-0a4l-9000000000-42841cd4af7434e568912021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 40V, Positive-QTOFsplash10-0a4r-9000000000-25b211098513e3ac7e1e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 10V, Negative-QTOFsplash10-0002-9000000000-b468460dca7829ea688f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 20V, Negative-QTOFsplash10-0002-9000000000-98095c9baf3499308c612021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - delta-Valerolactone 40V, Negative-QTOFsplash10-0006-9000000000-11bb130a3149d9b99b852021-10-12Wishart 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 IDNot Available
Chemspider IDNot Available
KEGG Compound IDC02240
BioCyc ID5-VALEROLACTONE
BiGG IDNot Available
Wikipedia LinkDelta-Valerolactone
METLIN IDNot Available
PubChem Compound10953
PDB IDNot Available
ChEBI ID16545
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 ]