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Showing metabocard for (-)-Corey lactone diol (HMDB0341202)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:40:13 UTC
Update Date2022-09-22 18:34:38 UTC
HMDB IDHMDB0341202
Secondary Accession NumbersNone
Metabolite Identification
Common Name(-)-Corey lactone diol
Description(-)-Corey lactone diol 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. Based on a literature review a small amount of articles have been published on (-)-Corey lactone diol.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341202 ((-)-Corey lactone diol)


  Mrv1652309092222182D          

 12 13  0  0  1  0            999 V2000
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7846   -1.0799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8792   -0.6674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971   -2.7326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3099   -0.6674    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
  1  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  4  9  1  6  0  0  0
  3 10  1  1  0  0  0
 10 11  1  0  0  0  0
  2 12  1  6  0  0  0
M  END
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3D MOL for HMDB0341202 ((-)-Corey lactone diol)

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3D SDF for HMDB0341202 ((-)-Corey lactone diol)

  Mrv1652309092222182D          

 12 13  0  0  1  0            999 V2000
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7846   -1.0799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8792   -0.6674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971   -2.7326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3099   -0.6674    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
  1  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  4  9  1  6  0  0  0
  3 10  1  1  0  0  0
 10 11  1  0  0  0  0
  2 12  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0341202

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1[C@H](O)C[C@@H]2OC(=O)C[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C8H12O4/c9-3-5-4-1-8(11)12-7(4)2-6(5)10/h4-7,9-10H,1-3H2/t4-,5-,6-,7+/m1/s1

> <INCHI_KEY>
VYTZWRCSPHQSFX-GBNDHIKLSA-N

> <FORMULA>
C8H12O4

> <MOLECULAR_WEIGHT>
172.18

> <EXACT_MASS>
172.073558866

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.650341918118002

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3aR,4S,5R,6aS)-5-hydroxy-4-(hydroxymethyl)-hexahydro-2H-cyclopenta[b]furan-2-one

> <JCHEM_LOGP>
-1.4997659473333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.571255241314724

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.680762725731554

> <JCHEM_PKA_STRONGEST_BASIC>
-2.634364777316395

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
39.8477

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3aR,4S,5R,6aS)-5-hydroxy-4-(hydroxymethyl)-hexahydrocyclopenta[b]furan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341202 ((-)-Corey lactone diol)
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PDB for HMDB0341202 ((-)-Corey lactone diol)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.905  -1.246   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000  -2.492   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.465  -2.016   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.929   0.000   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.374  -1.246   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.929  -2.492   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.476  -3.956   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.555  -5.101   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.445  -1.246   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    4                                                       
CONECT   10    3   11                                                       
CONECT   11   10                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

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3D PDB for HMDB0341202 ((-)-Corey lactone diol)
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SMILES for HMDB0341202 ((-)-Corey lactone diol)
OC[C@H]1[C@H](O)C[C@@H]2OC(=O)C[C@H]12
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INCHI for HMDB0341202 ((-)-Corey lactone diol)
InChI=1S/C8H12O4/c9-3-5-4-1-8(11)12-7(4)2-6(5)10/h4-7,9-10H,1-3H2/t4-,5-,6-,7+/m1/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H12O4
Average Molecular Weight172.18
Monoisotopic Molecular Weight172.073558866
IUPAC Name(3aR,4S,5R,6aS)-5-hydroxy-4-(hydroxymethyl)-hexahydro-2H-cyclopenta[b]furan-2-one
Traditional Name(3aR,4S,5R,6aS)-5-hydroxy-4-(hydroxymethyl)-hexahydrocyclopenta[b]furan-2-one
CAS Registry NumberNot Available
SMILES
OC[C@H]1[C@H](O)C[C@@H]2OC(=O)C[C@H]12
InChI Identifier
InChI=1S/C8H12O4/c9-3-5-4-1-8(11)12-7(4)2-6(5)10/h4-7,9-10H,1-3H2/t4-,5-,6-,7+/m1/s1
InChI KeyVYTZWRCSPHQSFX-GBNDHIKLSA-N
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
    • 

  • Cyclic alcohol
    • 

  • Tetrahydrofuran
    • 

  • Carboxylic acid ester
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Oxacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot 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
logP-1.5ChemAxon
pKa (Strongest Acidic)14.68ChemAxon
pKa (Strongest Basic)-2.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity39.85 m³·mol⁻¹ChemAxon
Polarizability16.65 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID2006592  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound2724453  
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. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]