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Showing metabocard for (3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one (HMDB0255328)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 14:57:21 UTC
Update Date2021-09-26 23:10:02 UTC
HMDB IDHMDB0255328
Secondary Accession NumbersNone
Metabolite Identification
Common Name(3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one
Description(3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one belongs to the class of organic compounds known as alpha-acyloxy ketones. These are ketones that have an acyloxy substituent alpha to the carbonyl group. They have the general structure R4C(=O)OC(R2)(R3)C(R1)=O (R1=organyl, R4=H or organyl; R2,R3 = any atom). Based on a literature review very few articles have been published on (3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). (3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

  Mrv1652309112116572D          

 12 12  0  0  0  0            999 V2000
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  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  0  0  0  0
  6 10  1  0  0  0  0
  5 11  1  0  0  0  0
  1 12  1  0  0  0  0
M  END
Download

3D MOL for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

HMDB0255328
     RDKit          3D
(3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one
 20 20  0  0  0  0  0  0  0  0999 V2000
   -1.9008    0.3676    2.4493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5145   -0.2046    1.3694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8044   -1.3889    1.2278 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1533   -1.1624    0.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2044   -0.2550    0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1512    0.1648    1.8956 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3676    0.1866   -0.0676 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2125    1.0279    0.6492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7062   -0.4385   -0.8284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3388   -1.4219   -1.6167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7452    0.2827   -0.0167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5783    1.6631   -0.1104 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5557   -2.1084   -0.1809 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9973    0.7767   -0.9520 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9369   -0.6764   -0.4836 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0269    1.9984    0.4614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    0.2094   -1.4335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8464   -0.9872   -2.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7812   -0.0344   -0.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3198    2.0004   -0.6730 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  2  0
  5  7  1  0
  7  8  1  0
  4  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11  2  1  0
  4 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 11 19  1  0
 12 20  1  0
M  END
Download

3D SDF for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

  Mrv1652309112116572D          

 12 12  0  0  0  0            999 V2000
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  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  0  0  0  0
  6 10  1  0  0  0  0
  5 11  1  0  0  0  0
  1 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255328

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h3-5,7,9-10H,1H2

> <INCHI_KEY>
PZTBFBJIHQUDGC-UHFFFAOYSA-N

> <FORMULA>
C6H8O6

> <MOLECULAR_WEIGHT>
176.124

> <EXACT_MASS>
176.032087978

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.792308481006623

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.73

> <JCHEM_LOGP>
-2.2822862293333337

> <ALOGPS_LOGS>
0.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.904290594653203

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.70686457785121

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3282489311399113

> <JCHEM_POLAR_SURFACE_AREA>
104.06000000000002

> <JCHEM_REFRACTIVITY>
33.937

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.81e+02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

HMDB0255328
     RDKit          3D
(3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one
 20 20  0  0  0  0  0  0  0  0999 V2000
   -1.9008    0.3676    2.4493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5145   -0.2046    1.3694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8044   -1.3889    1.2278 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1533   -1.1624    0.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2044   -0.2550    0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1512    0.1648    1.8956 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3676    0.1866   -0.0676 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2125    1.0279    0.6492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7062   -0.4385   -0.8284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3388   -1.4219   -1.6167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7452    0.2827   -0.0167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5783    1.6631   -0.1104 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5557   -2.1084   -0.1809 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9973    0.7767   -0.9520 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9369   -0.6764   -0.4836 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0269    1.9984    0.4614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    0.2094   -1.4335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8464   -0.9872   -2.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7812   -0.0344   -0.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3198    2.0004   -0.6730 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  2  0
  5  7  1  0
  7  8  1  0
  4  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11  2  1  0
  4 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 11 19  1  0
 12 20  1  0
M  END
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PDB for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       2.393   4.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.393   5.930   0.000  0.00  0.00           O+0
CONECT    1    2   12                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    4                                                       
CONECT   10    6                                                            
CONECT   11    5                                                            
CONECT   12    1                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

COMPND    HMDB0255328
HETATM    1  O1  UNL     1      -1.901   0.368   2.449  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.514  -0.205   1.369  1.00  0.00           C  
HETATM    3  O2  UNL     1      -0.804  -1.389   1.228  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.153  -1.162   0.209  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.204  -0.255   0.750  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.151   0.165   1.896  1.00  0.00           O  
HETATM    7  C4  UNL     1       2.368   0.187  -0.068  1.00  0.00           C  
HETATM    8  O4  UNL     1       3.213   1.028   0.649  1.00  0.00           O  
HETATM    9  C5  UNL     1      -0.706  -0.438  -0.828  1.00  0.00           C  
HETATM   10  O5  UNL     1      -1.339  -1.422  -1.617  1.00  0.00           O  
HETATM   11  C6  UNL     1      -1.745   0.283  -0.017  1.00  0.00           C  
HETATM   12  O6  UNL     1      -1.578   1.663  -0.110  1.00  0.00           O  
HETATM   13  H1  UNL     1       0.556  -2.108  -0.181  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.997   0.777  -0.952  1.00  0.00           H  
HETATM   15  H3  UNL     1       2.937  -0.676  -0.484  1.00  0.00           H  
HETATM   16  H4  UNL     1       3.027   1.998   0.461  1.00  0.00           H  
HETATM   17  H5  UNL     1      -0.070   0.209  -1.433  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.846  -0.987  -2.343  1.00  0.00           H  
HETATM   19  H7  UNL     1      -2.781  -0.034  -0.306  1.00  0.00           H  
HETATM   20  H8  UNL     1      -2.320   2.000  -0.673  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4
CONECT    4    5    9   13
CONECT    5    6    6    7
CONECT    7    8   14   15
CONECT    8   16
CONECT    9   10   11   17
CONECT   10   18
CONECT   11   12   19
CONECT   12   20
END
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SMILES for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

OCC(=O)C1OC(=O)C(O)C1O
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INCHI for HMDB0255328 ((3S,4R,5S)-3,4-Dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one)

InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h3-5,7,9-10H,1H2
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H8O6
Average Molecular Weight176.124
Monoisotopic Molecular Weight176.032087978
IUPAC Name3,4-dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one
Traditional Name3,4-dihydroxy-5-(2-hydroxyacetyl)oxolan-2-one
CAS Registry NumberNot Available
SMILES
OCC(=O)C1OC(=O)C(O)C1O
InChI Identifier
InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h3-5,7,9-10H,1H2
InChI KeyPZTBFBJIHQUDGC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha-acyloxy ketones. These are ketones that have an acyloxy substituent alpha to the carbonyl group. They have the general structure R4C(=O)OC(R2)(R3)C(R1)=O (R1=organyl, R4=H or organyl; R2,R3 = any atom).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentAlpha-acyloxy ketones
Alternative Parents
Substituents
  • Alpha-acyloxy ketone
  • Gamma butyrolactone
  • Monosaccharide
  • Alpha-hydroxy ketone
  • Oxolane
  • 1,2-diol
  • Carboxylic acid ester
  • Secondary alcohol
  • Ketone
  • Lactone
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Alcohol
  • Primary alcohol
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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 Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
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 IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound76135744
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]