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Showing metabocard for delta-Hexanolactone (HMDB0000453)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:51 UTC
HMDB IDHMDB0000453
Secondary Accession Numbers
  • HMDB00453
Metabolite Identification
Common Namedelta-Hexanolactone
Descriptiondelta-Hexanolactone is the lactone of 5-hydroxyhexanoic acid. Lactones are internal esters that exist in equilibrium between their closed (lactone) and open (hydroxy acid) forms in an aqueous environment. The lactone/hydroxy acid ratio at equilibrium is pH-dependent, with the closed form being favored at lower pH values, and can be greatly influenced by structural features of the lactone such as the ring size, substituents on the ring and the presence of double bonds within the ring. Many drugs and endogenous compounds are lactones or hydroxy acids and an enzyme capable of catalyzing the interchange between the open and closed forms in vivo could have pronounced effects upon their biological activity and/or distribution. delta-Hexanolactone is the substrate of paraoxonases (PON) in humans. Human PON1 hydrolyzes over 30 different lactones (cyclic esters) and catalyzes the reverse reaction (lactonization) of a broad range of hydroxy acids. Hydroxy acid lactonization or lactone hydrolysis is catalyzed until equilibrium between the open and closed forms is reached (PMID: 15772423 , 12963475 , 12963475 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000453 (delta-Hexanolactone)

5-Hydroxyhexanoic acid lactone.mol
  Mrv1652305271900082D          

  8  8  0  0  0  0            999 V2000
    0.7145    0.4125    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   -0.8250    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
   -0.7145    0.4125    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    0.8250    0.0000 O   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  1  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
  1  7  2  0  0  0  0
  1  8  1  0  0  0  0
  5  8  1  0  0  0  0
M  END
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3D MOL for HMDB0000453 (delta-Hexanolactone)

HMDB0000453
     RDKit          3D
delta-Hexanolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.0802    0.4916   -0.0985 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9178   -0.3702   -0.6048 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1909   -1.0340    0.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8464   -0.0785    1.0685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8856    0.0931   -0.0474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1612    0.8640   -1.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7682    1.8291   -1.6128 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1172    0.4642   -1.3978 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7015   -0.1857    0.5372 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6115    0.8381   -0.9984 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6444    1.3128    0.5068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3783   -1.1262   -1.2664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8678   -1.2758    1.3650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3228   -1.9391    0.1241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3118   -0.4261    1.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3049    0.9007    1.2034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1073   -0.9160   -0.5020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016    0.5577    0.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
M  END
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3D SDF for HMDB0000453 (delta-Hexanolactone)

5-Hydroxyhexanoic acid lactone.mol
  Mrv1652305271900082D          

  8  8  0  0  0  0            999 V2000
    0.7145    0.4125    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   -0.8250    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
   -0.7145    0.4125    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    0.8250    0.0000 O   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  1  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
  1  7  2  0  0  0  0
  1  8  1  0  0  0  0
  5  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000453

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CCCC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O2/c1-5-3-2-4-6(7)8-5/h5H,2-4H2,1H3

> <INCHI_KEY>
RZTOWFMDBDPERY-UHFFFAOYSA-N

> <FORMULA>
C6H10O2

> <MOLECULAR_WEIGHT>
114.1424

> <EXACT_MASS>
114.068079564

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.122193225175327

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-methyloxan-2-one

> <ALOGPS_LOGP>
0.93

> <JCHEM_LOGP>
1.010694995333333

> <ALOGPS_LOGS>
-0.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.0409063905943965

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
29.327900000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.41e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hexanolactone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0000453 (delta-Hexanolactone)

HMDB0000453
     RDKit          3D
delta-Hexanolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.0802    0.4916   -0.0985 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9178   -0.3702   -0.6048 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1909   -1.0340    0.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8464   -0.0785    1.0685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8856    0.0931   -0.0474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1612    0.8640   -1.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7682    1.8291   -1.6128 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1172    0.4642   -1.3978 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7015   -0.1857    0.5372 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6115    0.8381   -0.9984 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6444    1.3128    0.5068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3783   -1.1262   -1.2664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8678   -1.2758    1.3650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3228   -1.9391    0.1241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3118   -0.4261    1.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3049    0.9007    1.2034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1073   -0.9160   -0.5020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016    0.5577    0.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
M  END
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PDB for HMDB0000453 (delta-Hexanolactone)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 5-Hydroxyhexanoic acid lactone.mol                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -0.770   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      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
CONECT    1    2    7    8                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5                                                            
CONECT    7    1                                                            
CONECT    8    1    5                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0000453 (delta-Hexanolactone)

COMPND    HMDB0000453
HETATM    1  C1  UNL     1       2.080   0.492  -0.099  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.918  -0.370  -0.605  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.191  -1.034   0.516  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.846  -0.078   1.068  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.886   0.093  -0.047  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.161   0.864  -1.088  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.768   1.829  -1.613  1.00  0.00           O  
HETATM    8  O2  UNL     1       0.117   0.464  -1.398  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.702  -0.186   0.537  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.612   0.838  -0.998  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.644   1.313   0.507  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.378  -1.126  -1.266  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.868  -1.276   1.365  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.323  -1.939   0.124  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.312  -0.426   1.995  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.305   0.901   1.203  1.00  0.00           H  
HETATM   17  H9  UNL     1      -2.107  -0.916  -0.502  1.00  0.00           H  
HETATM   18  H10 UNL     1      -2.802   0.558   0.300  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    8   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7    7    8
END
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SMILES for HMDB0000453 (delta-Hexanolactone)

CC1CCCC(=O)O1
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INCHI for HMDB0000453 (delta-Hexanolactone)

InChI=1S/C6H10O2/c1-5-3-2-4-6(7)8-5/h5H,2-4H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H10O2
Average Molecular Weight114.1424
Monoisotopic Molecular Weight114.068079564
IUPAC Name6-methyloxan-2-one
Traditional Namehexanolactone
CAS Registry Number823-22-3
SMILES
CC1CCCC(=O)O1
InChI Identifier
InChI=1S/C6H10O2/c1-5-3-2-4-6(7)8-5/h5H,2-4H2,1H3
InChI KeyRZTOWFMDBDPERY-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 DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point31.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Boiling Point110.00 to 112.00 °C. @ 15.00 mm HgThe Good Scents Company Information System
Water Solubility32190 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.431 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008078
KNApSAcK IDC00054812
Chemspider ID12649
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5442
PubChem Compound13204
PDB IDNot Available
ChEBI ID589927
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1026381
References
Synthesis ReferenceMink, Daniel; Wolberg, Michael; Schuermann, Martin; Hilker, Iris. Chemoenzymic preparation of d-lactones. PCT Int. Appl. (2007), 40pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Draganov DI, Teiber JF, Speelman A, Osawa Y, Sunahara R, La Du BN: Human paraoxonases (PON1, PON2, and PON3) are lactonases with overlapping and distinct substrate specificities. J Lipid Res. 2005 Jun;46(6):1239-47. Epub 2005 Mar 16. [PubMed:15772423 ]
  2. Moser AB, Jones DS, Raymond GV, Moser HW: Plasma and red blood cell fatty acids in peroxisomal disorders. Neurochem Res. 1999 Feb;24(2):187-97. [PubMed:9972864 ]
  3. Teiber JF, Draganov DI, La Du BN: Lactonase and lactonizing activities of human serum paraoxonase (PON1) and rabbit serum PON3. Biochem Pharmacol. 2003 Sep 15;66(6):887-96. [PubMed:12963475 ]