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Showing metabocard for 1-Rhamnono-1,4-lactone (HMDB0302823)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 20:57:15 UTC
Update Date2021-09-23 20:57:15 UTC
HMDB IDHMDB0302823
Secondary Accession NumbersNone
Metabolite Identification
Common Name1-Rhamnono-1,4-lactone
Description1-rhamnono-1,4-lactone is a member of the class of 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. 1-rhamnono-1,4-lactone is soluble (in water) and a very weakly acidic compound (based on its pKa). 1-rhamnono-1,4-lactone can be found in rice, which makes 1-rhamnono-1,4-lactone a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302823 (1-Rhamnono-1,4-lactone)

  Mrv0541 02241223382D          

 11 11  0  0  0  0            999 V2000
    0.1235    0.3299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6189   -0.3299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1235   -0.9905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5363   -1.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3620    0.4950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6189    0.0822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6189   -0.7428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3620   -1.1556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1235    1.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5363    1.0730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3620    1.0730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  7  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0302823 (1-Rhamnono-1,4-lactone)

HMDB0302823
     RDKit          3D
1-Rhamnono-1,4-lactone
 21 21  0  0  0  0  0  0  0  0999 V2000
   -2.0008   -0.2190   -0.5445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4139    0.5009    0.6328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0582   -0.0105    1.7812 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0587    0.2228    0.8178 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2707   -1.1654    0.9385 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8767   -1.6133   -0.2232 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7309   -2.7710   -0.6824 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6695   -0.4713   -0.7341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9532   -0.4657   -0.1935 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9085    0.7309   -0.2860 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2166    1.3702   -1.2992 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8254    0.4326   -0.9534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2760   -0.4280   -1.3468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5385   -1.1629   -0.2345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5942    1.5723    0.5680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4214   -0.0241    2.5616 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3673    0.6792    1.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7775   -0.5450   -1.8331 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9533   -0.3060    0.7698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6494    1.4841    0.1071 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6959    2.1893   -1.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  4  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  3 16  1  0
  4 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
M  END
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3D SDF for HMDB0302823 (1-Rhamnono-1,4-lactone)

  Mrv0541 02241223382D          

 11 11  0  0  0  0            999 V2000
    0.1235    0.3299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6189   -0.3299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1235   -0.9905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5363   -1.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3620    0.4950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6189    0.0822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6189   -0.7428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3620   -1.1556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1235    1.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5363    1.0730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3620    1.0730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  7  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302823

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C1OC(=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c1-2(7)5-3(8)4(9)6(10)11-5/h2-5,7-9H,1H3

> <INCHI_KEY>
VASLEPDZAKCNJX-UHFFFAOYSA-N

> <FORMULA>
C6H10O5

> <MOLECULAR_WEIGHT>
162.1406

> <EXACT_MASS>
162.05282343

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
14.6702658876053

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydroxy-5-(1-hydroxyethyl)oxolan-2-one

> <ALOGPS_LOGP>
-1.62

> <JCHEM_LOGP>
-1.6983632193333331

> <ALOGPS_LOGS>
0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.630963283447127

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.63249703131222

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0639700858110572

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
33.2351

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.31e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dihydroxy-5-(1-hydroxyethyl)oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0302823 (1-Rhamnono-1,4-lactone)

HMDB0302823
     RDKit          3D
1-Rhamnono-1,4-lactone
 21 21  0  0  0  0  0  0  0  0999 V2000
   -2.0008   -0.2190   -0.5445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4139    0.5009    0.6328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0582   -0.0105    1.7812 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0587    0.2228    0.8178 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2707   -1.1654    0.9385 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8767   -1.6133   -0.2232 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7309   -2.7710   -0.6824 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6695   -0.4713   -0.7341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9532   -0.4657   -0.1935 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9085    0.7309   -0.2860 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2166    1.3702   -1.2992 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8254    0.4326   -0.9534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2760   -0.4280   -1.3468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5385   -1.1629   -0.2345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5942    1.5723    0.5680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4214   -0.0241    2.5616 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3673    0.6792    1.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7775   -0.5450   -1.8331 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9533   -0.3060    0.7698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6494    1.4841    0.1071 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6959    2.1893   -1.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  4  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  3 16  1  0
  4 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
M  END
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PDB for HMDB0302823 (1-Rhamnono-1,4-lactone)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       0.231   0.616   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.155  -0.616   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.231  -1.849   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.001  -3.236   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -2.542   0.924   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.155   0.153   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.155  -1.387   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.542  -2.157   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.231   3.236   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.001   2.003   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.542   2.003   0.000  0.00  0.00           C+0
CONECT    1    2    6   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3                                                            
CONECT    5    6                                                            
CONECT    6    1    5    7                                                  
CONECT    7    3    6    8                                                  
CONECT    8    7                                                            
CONECT    9   10                                                            
CONECT   10    1    9   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for HMDB0302823 (1-Rhamnono-1,4-lactone)

COMPND    HMDB0302823
HETATM    1  C1  UNL     1      -2.001  -0.219  -0.544  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.414   0.501   0.633  1.00  0.00           C  
HETATM    3  O1  UNL     1      -2.058  -0.011   1.781  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.059   0.223   0.818  1.00  0.00           C  
HETATM    5  O2  UNL     1       0.271  -1.165   0.938  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.877  -1.613  -0.223  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.731  -2.771  -0.682  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.670  -0.471  -0.734  1.00  0.00           C  
HETATM    9  O4  UNL     1       2.953  -0.466  -0.194  1.00  0.00           O  
HETATM   10  C6  UNL     1       0.909   0.731  -0.286  1.00  0.00           C  
HETATM   11  O5  UNL     1       0.217   1.370  -1.299  1.00  0.00           O  
HETATM   12  H1  UNL     1      -2.825   0.433  -0.953  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.276  -0.428  -1.347  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.539  -1.163  -0.235  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.594   1.572   0.568  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.421  -0.024   2.562  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.367   0.679   1.780  1.00  0.00           H  
HETATM   18  H7  UNL     1       1.778  -0.545  -1.833  1.00  0.00           H  
HETATM   19  H8  UNL     1       2.953  -0.306   0.770  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.649   1.484   0.107  1.00  0.00           H  
HETATM   21  H10 UNL     1       0.696   2.189  -1.626  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4   15
CONECT    3   16
CONECT    4    5   10   17
CONECT    5    6
CONECT    6    7    7    8
CONECT    8    9   10   18
CONECT    9   19
CONECT   10   11   20
CONECT   11   21
END
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SMILES for HMDB0302823 (1-Rhamnono-1,4-lactone)

CC(O)C1OC(=O)C(O)C1O
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INCHI for HMDB0302823 (1-Rhamnono-1,4-lactone)

InChI=1S/C6H10O5/c1-2(7)5-3(8)4(9)6(10)11-5/h2-5,7-9H,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H10O5
Average Molecular Weight162.1406
Monoisotopic Molecular Weight162.05282343
IUPAC Name3,4-dihydroxy-5-(1-hydroxyethyl)oxolan-2-one
Traditional Name3,4-dihydroxy-5-(1-hydroxyethyl)oxolan-2-one
CAS Registry NumberNot Available
SMILES
CC(O)C1OC(=O)C(O)C1O
InChI Identifier
InChI=1S/C6H10O5/c1-2(7)5-3(8)4(9)6(10)11-5/h2-5,7-9H,1H3
InChI KeyVASLEPDZAKCNJX-UHFFFAOYSA-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
  • Tetrahydrofuran
  • Secondary alcohol
  • Carboxylic acid ester
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • 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 IDFDB006380
KNApSAcK IDNot Available
Chemspider ID212003
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound242516
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 ReferencesNot Available