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Showing metabocard for epsilon-Caprolactone (HMDB0060476)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:23:34 UTC
Update Date2023-02-21 17:30:02 UTC
HMDB IDHMDB0060476
Secondary Accession Numbers
  • HMDB60476
Metabolite Identification
Common Nameepsilon-Caprolactone
Descriptionε-Caprolactone, also known simply as caprolactone, is a compound belonging to the family of compounds known as lactones. Lactones are cyclic esters of hydroxyl carboxylic acids, wherein the functional group has become part of a ring structure with carbon atoms. Caprolactone consists of a seven membered ring derived from the cyclization of caproic acid. As a monomer it used in the production of highly specialized plastics and polymers. Caprolactone is produced by the Baeyer-Villiger oxidation of cyclohexanone with peracetic acid, and was used previously (until economically inviable) as a precursor in the production of caprolactam. Several other caprolactone isomers are known. These isomers include α-, β-, γ-, and δ-caprolactones. All are chiral. (R)-γ-caprolactone is a component of floral scents and of the aromas of some fruits and vegetables (Journal of Agricultural and Food Chemistry. 37: 413–418), while δ-caprolactone is found in heated milk fat (Journal of Dairy Science. 48 (5): 615–616).
Structure
Data?1677000602
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060476 (epsilon-Caprolactone)

  Mrv0541 05161318232D          

  8  8  0  0  0  0            999 V2000
    1.2691   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7834    0.2009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4441   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5999    1.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0703    0.2009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8566    1.3632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8566    2.1882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1133    1.0053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  2  0  0  0  0
  8  5  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
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3D MOL for HMDB0060476 (epsilon-Caprolactone)

HMDB0060476
     RDKit          3D
epsilon-Caprolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.2400   -1.9814    0.0616 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2487   -1.1803    0.0066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6552    0.2140   -0.0176 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6313    1.2090    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6691    1.0602   -0.3518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4634   -0.0193    0.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2075   -1.3061   -0.3543 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0447   -1.8531   -0.0156 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5194    0.3173    0.7030 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1086    0.4943   -1.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0230    2.2241    0.1526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4464    1.1896    1.4774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2572    1.9861   -0.3453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4764    0.7972   -1.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5203    0.2363    0.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0819   -0.1422    1.4200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2599   -1.2016   -1.4594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9815   -2.0440   -0.0109 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  8  1  0
  8  2  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
M  END
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3D SDF for HMDB0060476 (epsilon-Caprolactone)

  Mrv0541 05161318232D          

  8  8  0  0  0  0            999 V2000
    1.2691   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7834    0.2009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4441   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5999    1.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0703    0.2009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8566    1.3632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8566    2.1882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1133    1.0053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  2  0  0  0  0
  8  5  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060476

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCCCCO1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O2/c7-6-4-2-1-3-5-8-6/h1-5H2

> <INCHI_KEY>
PAPBSGBWRJIAAV-UHFFFAOYSA-N

> <FORMULA>
C6H10O2

> <MOLECULAR_WEIGHT>
114.1424

> <EXACT_MASS>
114.068079564

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
11.987251306226336

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oxepan-2-one

> <ALOGPS_LOGP>
0.51

> <JCHEM_LOGP>
1.0386886356666667

> <ALOGPS_LOGS>
-0.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.032727987178912

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
29.5101

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.32e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
caprolactone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0060476 (epsilon-Caprolactone)

HMDB0060476
     RDKit          3D
epsilon-Caprolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.2400   -1.9814    0.0616 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2487   -1.1803    0.0066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6552    0.2140   -0.0176 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6313    1.2090    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6691    1.0602   -0.3518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4634   -0.0193    0.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2075   -1.3061   -0.3543 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0447   -1.8531   -0.0156 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5194    0.3173    0.7030 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1086    0.4943   -1.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0230    2.2241    0.1526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4464    1.1896    1.4774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2572    1.9861   -0.3453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4764    0.7972   -1.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5203    0.2363    0.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0819   -0.1422    1.4200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2599   -1.2016   -1.4594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9815   -2.0440   -0.0109 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  8  1  0
  8  2  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
M  END
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PDB for HMDB0060476 (epsilon-Caprolactone)

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       2.369  -0.829   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.329   0.375   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.829  -0.829   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.986   1.877   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.131   0.375   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.599   2.545   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.599   4.085   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.211   1.877   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    8                                                       
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0060476 (epsilon-Caprolactone)

COMPND    HMDB0060476
HETATM    1  O1  UNL     1       2.240  -1.981   0.062  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.249  -1.180   0.007  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.655   0.214  -0.018  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.631   1.209   0.372  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.669   1.060  -0.352  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.463  -0.019   0.365  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.208  -1.306  -0.354  1.00  0.00           C  
HETATM    8  O2  UNL     1       0.045  -1.853  -0.016  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.519   0.317   0.703  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.109   0.494  -1.012  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.023   2.224   0.153  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.446   1.190   1.477  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.257   1.986  -0.345  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.476   0.797  -1.414  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.520   0.236   0.423  1.00  0.00           H  
HETATM   16  H8  UNL     1      -1.082  -0.142   1.420  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.260  -1.202  -1.459  1.00  0.00           H  
HETATM   18  H10 UNL     1      -1.982  -2.044  -0.011  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6    7   15   16
CONECT    7    8   17   18
END
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SMILES for HMDB0060476 (epsilon-Caprolactone)

O=C1CCCCCO1
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INCHI for HMDB0060476 (epsilon-Caprolactone)

InChI=1S/C6H10O2/c7-6-4-2-1-3-5-8-6/h1-5H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H10O2
Average Molecular Weight114.1424
Monoisotopic Molecular Weight114.068079564
IUPAC Nameoxepan-2-one
Traditional Namecaprolactone
CAS Registry NumberNot Available
SMILES
O=C1CCCCCO1
InChI Identifier
InChI=1S/C6H10O2/c7-6-4-2-1-3-5-8-6/h1-5H2
InChI KeyPAPBSGBWRJIAAV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as lactones. These are cyclic esters of hydroxy carboxylic acids, containing a 1-oxacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassLactones
Sub ClassNot Available
Direct ParentLactones
Alternative Parents
Substituents
  • Caprolactone
  • Oxepane
  • 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 Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
Predicted Chromatographic Properties
Spectra
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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC01880
BioCyc IDCPD-101
BiGG IDNot Available
Wikipedia LinkCaprolactone
METLIN IDNot Available
PubChem Compound10401
PDB IDNot Available
ChEBI ID17915
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. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details
1. Regucalcin
General function:
Involved in calcium ion binding
Specific function:
Gluconolactonase with low activity towards other sugar lactones, including gulonolactone and galactonolactone. Can also hydrolyze diisopropyl phosphorofluoridate and phenylacetate (in vitro). Calcium-binding protein. Modulates Ca(2+) signaling, and Ca(2+)-dependent cellular processes and enzyme activities (By similarity).
Gene Name:
RGN
Uniprot ID:
Q15493
Molecular weight:
33252.53
Reactions
epsilon-Caprolactone + Water → 6-Hydroxyhexanoic aciddetails