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Showing metabocard for 5-Hydroxy-4-pentenoic acid d-lactone (HMDB0040145)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:41:25 UTC
Update Date2023-02-21 17:27:45 UTC
HMDB IDHMDB0040145
Secondary Accession Numbers
  • HMDB40145
Metabolite Identification
Common Name5-Hydroxy-4-pentenoic acid d-lactone
Description5-Hydroxy-4-pentenoic acid d-lactone belongs to the class of organic compounds known as dihydropyranones. Dihydropyranones are compounds containing a hydrogenated pyran ring which bears a ketone, and contains one double bond. 5-Hydroxy-4-pentenoic acid d-lactone has been detected, but not quantified in, nuts. This could make 5-hydroxy-4-pentenoic acid D-lactone a potential biomarker for the consumption of these foods. Based on a literature review a small amount of articles have been published on 5-Hydroxy-4-pentenoic acid d-lactone.
Structure
Data?1677000465
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)


  Mrv0541 05061311392D          

  7  7  0  0  0  0            999 V2000
   -0.7703   -0.8246    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4835   -0.4122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4835    0.4123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1981    0.8246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9128    0.4123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9128   -0.4122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1981   -0.8246    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
  2  7  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
M  END
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3D MOL for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)

HMDB0040145
     RDKit          3D
5-Hydroxy-4-pentenoic acid d-lactone
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.3186    2.2274    0.7364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5151    1.4154    0.2168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0385    0.2745   -0.5769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4474   -0.9809    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0302   -0.8725    0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6207    0.3054    0.2697 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8663    1.4711    0.3079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1376    0.1801   -0.4872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7179    0.4143   -1.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7216   -1.8786   -0.5437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9301   -1.0438    1.0621 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6116   -1.8047    0.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6980    0.2924    0.3366 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  2  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
  6 13  1  0
M  END
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3D SDF for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)


  Mrv0541 05061311392D          

  7  7  0  0  0  0            999 V2000
   -0.7703   -0.8246    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4835   -0.4122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4835    0.4123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1981    0.8246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9128    0.4123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9128   -0.4122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1981   -0.8246    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
  2  7  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040145

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCC=CO1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O2/c6-5-3-1-2-4-7-5/h2,4H,1,3H2

> <INCHI_KEY>
VEFDLKXOSOFUIN-UHFFFAOYSA-N

> <FORMULA>
C5H6O2

> <MOLECULAR_WEIGHT>
98.0999

> <EXACT_MASS>
98.036779436

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
9.329548385970492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydro-2H-pyran-2-one

> <ALOGPS_LOGP>
0.63

> <JCHEM_LOGP>
0.6060990156666666

> <ALOGPS_LOGS>
0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.15911865169973

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
25.0022

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dihydropyran-2-one

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)

HMDB0040145
     RDKit          3D
5-Hydroxy-4-pentenoic acid d-lactone
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.3186    2.2274    0.7364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5151    1.4154    0.2168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0385    0.2745   -0.5769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4474   -0.9809    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0302   -0.8725    0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6207    0.3054    0.2697 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8663    1.4711    0.3079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1376    0.1801   -0.4872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7179    0.4143   -1.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7216   -1.8786   -0.5437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9301   -1.0438    1.0621 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6116   -1.8047    0.1140 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6980    0.2924    0.3366 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  2  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
  6 13  1  0
M  END
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PDB for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)

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  O   UNK     0      -1.438  -1.539   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.769  -0.769   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.769   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.103   1.539   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.437   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.437  -0.769   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -4.103  -1.539   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    2    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)

COMPND    HMDB0040145
HETATM    1  O1  UNL     1      -1.319   2.227   0.736  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.515   1.415   0.217  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.038   0.275  -0.577  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.447  -0.981   0.045  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.030  -0.872   0.146  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.621   0.305   0.270  1.00  0.00           C  
HETATM    7  O2  UNL     1       0.866   1.471   0.308  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.138   0.180  -0.487  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.718   0.414  -1.627  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.722  -1.879  -0.544  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.930  -1.044   1.062  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.612  -1.805   0.114  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.698   0.292   0.337  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    6   12
CONECT    6    7   13
END
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SMILES for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)

O=C1CCC=CO1
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INCHI for HMDB0040145 (5-Hydroxy-4-pentenoic acid d-lactone)

InChI=1S/C5H6O2/c6-5-3-1-2-4-7-5/h2,4H,1,3H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5-Hydroxy-4-pentenoate D-lactoneGenerator
3,4-dihydro-2H-Pyran-2-oneHMDB
4,5-DehydrovalerolactoneHMDB
Chemical FormulaC5H6O2
Average Molecular Weight98.0999
Monoisotopic Molecular Weight98.036779436
IUPAC Name3,4-dihydro-2H-pyran-2-one
Traditional Name3,4-dihydropyran-2-one
CAS Registry Number26638-97-1
SMILES
O=C1CCC=CO1
InChI Identifier
InChI=1S/C5H6O2/c6-5-3-1-2-4-7-5/h2,4H,1,3H2
InChI KeyVEFDLKXOSOFUIN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dihydropyranones. Dihydropyranones are compounds containing a hydrogenated pyran ring which bears a ketone, and contains one double bond.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrans
Sub ClassPyranones and derivatives
Direct ParentDihydropyranones
Alternative Parents
Substituents
  • Dihydropyranone
  • Enol ester
  • Lactone
  • 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 DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Route 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 Solubility111 g/LALOGPS
logP0.63ALOGPS
logP0.61ChemAxon
logS0.05ALOGPS
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity25 m³·mol⁻¹ChemAxon
Polarizability9.33 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]+118.69131661259
DarkChem[M-H]-112.43431661259
DeepCCS[M+H]+126.16630932474
DeepCCS[M-H]-124.22230932474
DeepCCS[M-2H]-159.65130932474
DeepCCS[M+Na]+133.97430932474
AllCCS[M+H]+120.132859911
AllCCS[M+H-H2O]+114.932859911
AllCCS[M+NH4]+124.932859911
AllCCS[M+Na]+126.332859911
AllCCS[M-H]-118.932859911
AllCCS[M+Na-2H]-122.032859911
AllCCS[M+HCOO]-125.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Hydroxy-4-pentenoic acid d-lactoneO=C1CCC=CO11670.4Standard polar33892256
5-Hydroxy-4-pentenoic acid d-lactoneO=C1CCC=CO1879.7Standard non polar33892256
5-Hydroxy-4-pentenoic acid d-lactoneO=C1CCC=CO1943.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f96-9000000000-5ad3b33be7840b413d122017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 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 - 5-Hydroxy-4-pentenoic acid d-lactone 10V, Negative-QTOFsplash10-0002-9000000000-1dec93d143339f4c6d6d2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 20V, Negative-QTOFsplash10-0002-9000000000-84edf5bdb01f32fe72112017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 40V, Negative-QTOFsplash10-0f6t-9000000000-d990c1265c6da25c87472017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 10V, Negative-QTOFsplash10-0002-9000000000-1d422a441afeaef289cc2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 20V, Negative-QTOFsplash10-0002-9000000000-f37870bebae3a6d3b8022021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 40V, Negative-QTOFsplash10-0006-9000000000-a8f70f260edaa8eb76e52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 10V, Positive-QTOFsplash10-0002-9000000000-7791bacbdee9190373412017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 20V, Positive-QTOFsplash10-0k9b-9000000000-f2dde8a4b16b2c463e062017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 40V, Positive-QTOFsplash10-000i-9000000000-4e83d81816e680b283f92017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 10V, Positive-QTOFsplash10-0002-9000000000-3e9d597959372beb50ef2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 20V, Positive-QTOFsplash10-0a4l-9000000000-02d5b26e1cf5016321cb2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxy-4-pentenoic acid d-lactone 40V, Positive-QTOFsplash10-0udu-9000000000-fb831b048f287e8df7972021-09-23Wishart 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 LocationsNot Available
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 IDFDB019842
KNApSAcK IDNot Available
Chemspider ID129648
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound147020
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.. .