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Showing NP-Card for Gamma-Caprolactone (NP0001058)

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Record Information
Version2.0
Created at2006-08-13 05:47:24 UTC
Updated at2024-09-17 15:43:56 UTC
NP-MRD IDNP0001058
Secondary Accession NumbersNone
Natural Product Identification
Common NameGamma-Caprolactone
DescriptionGamma-Caprolactone, also known as 4-ethyl-4-butanolide or 4-hexanolide, belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. Thus, Gamma-caprolactone is considered to be a fatty ester lipid molecule. Gamma-Caprolactone is a very hydrophobic molecule, practically insoluble in water, and relatively neutral. Gamma-Caprolactone exists in all eukaryotes, ranging from yeast to humans. Outside of the human body, Gamma-caprolactone has been detected, but not quantified in several different foods, such as potato, cereals and cereal products, pomes, alcoholic beverages, and fruits. It is occasionally found as a volatile component of human urine. In some cases differences up to an order of magnitude are observed. It has been also found in the polar fraction of human blood.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001058 (Gamma-Caprolactone)


  Mrv1652305271900132D          

  8  8  0  0  0  0            999 V2000
   26.2050  -11.6566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.7530  -11.4267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.8723  -11.1716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.6175  -10.3871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7925  -10.3871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6569  -11.4267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5376  -11.1716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2700  -10.8746    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  2  7  2  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
Download

3D MOL for NP0001058 (Gamma-Caprolactone)

HMDB0003843
     RDKit          3D
Gamma-Caprolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
   -2.4461    0.6256    0.0250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4055   -0.2853    0.6179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -0.0707   -0.0971 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9715   -0.9750    0.4764 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2115   -0.3332   -0.1306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8271    1.1052   -0.1188 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6226    2.0571   -0.3371 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4586    1.2035    0.1711 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1743    0.0019   -0.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135    1.3585   -0.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9565    1.1425    0.8746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2774   -0.1299    1.7146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6745   -1.3598    0.4854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2255   -0.2403   -1.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9457   -0.8494    1.5802 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8326   -2.0158    0.1627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1156   -0.5312    0.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2901   -0.7038   -1.1703 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  3  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 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
Download

3D SDF for NP0001058 (Gamma-Caprolactone)


  Mrv1652305271900132D          

  8  8  0  0  0  0            999 V2000
   26.2050  -11.6566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.7530  -11.4267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.8723  -11.1716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.6175  -10.3871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7925  -10.3871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6569  -11.4267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5376  -11.1716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2700  -10.8746    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  2  7  2  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001058

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC1CCC(=O)O1

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

> <INCHI_KEY>
JBFHTYHTHYHCDJ-UHFFFAOYSA-N

> <FORMULA>
C6H10O2

> <MOLECULAR_WEIGHT>
114.1424

> <EXACT_MASS>
114.068079564

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.15642395669613

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-ethyloxolan-2-one

> <ALOGPS_LOGP>
0.77

> <JCHEM_LOGP>
1.0886487253333332

> <ALOGPS_LOGS>
-0.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.042532034562416

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
29.2509

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.24e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gamma-hexalactone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0001058 (Gamma-Caprolactone)

HMDB0003843
     RDKit          3D
Gamma-Caprolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
   -2.4461    0.6256    0.0250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4055   -0.2853    0.6179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -0.0707   -0.0971 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9715   -0.9750    0.4764 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2115   -0.3332   -0.1306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8271    1.1052   -0.1188 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6226    2.0571   -0.3371 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4586    1.2035    0.1711 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1743    0.0019   -0.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135    1.3585   -0.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9565    1.1425    0.8746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2774   -0.1299    1.7146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6745   -1.3598    0.4854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2255   -0.2403   -1.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9457   -0.8494    1.5802 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8326   -2.0158    0.1627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1156   -0.5312    0.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2901   -0.7038   -1.1703 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  3  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 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
Download

PDB for NP0001058 (Gamma-Caprolactone)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      48.916 -21.759   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      46.206 -21.330   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      50.162 -20.854   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      49.686 -19.389   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      48.146 -19.389   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      51.626 -21.330   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      47.670 -20.854   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      52.771 -20.299   0.000  0.00  0.00           C+0
CONECT    1    3    7                                                       
CONECT    2    7                                                            
CONECT    3    1    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4    7                                                       
CONECT    6    3    8                                                       
CONECT    7    1    2    5                                                  
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for NP0001058 (Gamma-Caprolactone)

COMPND    HMDB0003843
HETATM    1  C1  UNL     1      -2.446   0.626   0.025  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.405  -0.285   0.618  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.102  -0.071  -0.097  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.971  -0.975   0.476  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.211  -0.333  -0.131  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.827   1.105  -0.119  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.623   2.057  -0.337  1.00  0.00           O  
HETATM    8  O2  UNL     1       0.459   1.204   0.171  1.00  0.00           O  
HETATM    9  H1  UNL     1      -3.174   0.002  -0.533  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.014   1.359  -0.690  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.957   1.142   0.875  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.277  -0.130   1.715  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.674  -1.360   0.485  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.226  -0.240  -1.169  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.946  -0.849   1.580  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.833  -2.016   0.163  1.00  0.00           H  
HETATM   17  H9  UNL     1       3.116  -0.531   0.469  1.00  0.00           H  
HETATM   18  H10 UNL     1       2.290  -0.704  -1.170  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4    8   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7    7    8
END
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SMILES for NP0001058 (Gamma-Caprolactone)

CCC1CCC(=O)O1
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INCHI for NP0001058 (Gamma-Caprolactone)

InChI=1S/C6H10O2/c1-2-5-3-4-6(7)8-5/h5H,2-4H2,1H3
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View in JSmolView NMR Assignments
Synonyms
ValueSource
4-Ethyl-4-butanolideChEBI
4-HexanolideChEBI
4-Hydroxyhexanoic acid lactoneChEBI
5-Ethyltetrahydro-2-furanoneChEBI
6-CaprolactoneChEBI
Dihydro-5-ethyl-2(3H)-furanoneChEBI
gamma-Ethyl-N-butyrolactoneChEBI
gamma-EthylbutyrolactoneChEBI
gamma-HexanolactoneChEBI
4-Hydroxyhexanoate lactoneGenerator
g-Ethyl-N-butyrolactoneGenerator
Γ-ethyl-N-butyrolactoneGenerator
g-EthylbutyrolactoneGenerator
Γ-ethylbutyrolactoneGenerator
g-HexanolactoneGenerator
Γ-hexanolactoneGenerator
g-CaprolactoneGenerator
Γ-caprolactoneGenerator
4-Ethylbutanolide (gamma-hexalactone)HMDB
4-Hydroxy-hexanoateHMDB
4-Hydroxy-hexanoic acidHMDB
4-Hydroxy-hexanoic acid gamma-lactoneHMDB
4-Hydroxy-hexanoic acid lactoneHMDB
4-HydroxyhexanoateHMDB
4-Hydroxyhexanoic acidHMDB
5-Ethyldihydro-2(3H)-furanoneHMDB
5-Ethyldihydrofuran-2(3H)-oneHMDB
gamma-Ethyl-gamma-butyrolactoneHMDB
gamma-HexalactoneHMDB
Hexa-4-olideHMDB
Hexanolide-1,4HMDB
TonkalideHMDB
ToukalideHMDB
Chemical FormulaC6H10O2
Average Mass114.1424 Da
Monoisotopic Mass114.06808 Da
IUPAC Name5-ethyloxolan-2-one
Traditional Namegamma-hexalactone
CAS Registry Number695-06-7
SMILES
CCC1CCC(=O)O1
InChI Identifier
InChI=1S/C6H10O2/c1-2-5-3-4-6(7)8-5/h5H,2-4H2,1H3
InChI KeyJBFHTYHTHYHCDJ-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Achillea abrotanoidesLOTUS Database
Aspergillus candidusLOTUS Database
Cannabis sativaCannabisDB
      Not Available
Coffea arabicaKNApSAcK Database
Coffea arabica L.Plant
Fusarium poaeLOTUS Database
Glycyrrhiza glabraLOTUS Database
Gossypium hirsutumLOTUS Database
Mangifera indicaLOTUS Database
Polygala senegaLOTUS Database
Scutellaria baicalensisLOTUS Database
Trigonella foenum-graecumLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassLactones
Sub ClassGamma butyrolactones
Direct ParentGamma butyrolactones
Alternative Parents
Substituents
  • Gamma butyrolactone
  • Tetrahydrofuran
  • 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
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point-18 °CNot Available
Boiling Point100.00 to 102.00 °C. @ 18.00 mm HgThe Good Scents Company Information System
Water Solubility0The Good Scents Company Information System
LogP0.413 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility22.4 g/LALOGPS
logP0.77ALOGPS
logP1.09ChemAxon
logS-0.71ALOGPS
pKa (Strongest Basic)-7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.25 m³·mol⁻¹ChemAxon
Polarizability12.16 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003843
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB008075
KNApSAcK IDC00053196
Chemspider ID12232
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12756
PDB IDNot Available
ChEBI ID85235
Good Scents IDrw1006382
References
General References
  1. Zlatkis A, Liebich HM: Profile of volatile metabolites in human urine. Clin Chem. 1971 Jul;17(7):592-4. [PubMed:5556886 ]
  2. Khersonsky O, Tawfik DS: Structure-reactivity studies of serum paraoxonase PON1 suggest that its native activity is lactonase. Biochemistry. 2005 Apr 26;44(16):6371-82. [PubMed:15835926 ]
  3. Thoma H, Reiner J, Spiteller G: Profiles of strongly polar and less polar acids obtained from human blood, plasma and serum by two-step ultrafiltration. J Chromatogr. 1984 Jul 13;309(1):17-32. [PubMed:6480763 ]
  4. Cirou A, Raffoux A, Diallo S, Latour X, Dessaux Y, Faure D: Gamma-caprolactone stimulates growth of quorum-quenching Rhodococcus populations in a large-scale hydroponic system for culturing Solanum tuberosum. Res Microbiol. 2011 Nov;162(9):945-50. doi: 10.1016/j.resmic.2011.01.010. Epub 2011 Feb 1. [PubMed:21288487 ]
  5. Barbey C, Crepin A, Cirou A, Budin-Verneuil A, Orange N, Feuilloley M, Faure D, Dessaux Y, Burini JF, Latour X: Catabolic pathway of gamma-caprolactone in the biocontrol agent Rhodococcus erythropolis. J Proteome Res. 2012 Jan 1;11(1):206-16. doi: 10.1021/pr200936q. Epub 2011 Dec 2. [PubMed:22085026 ]