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Showing metabocard for (2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol (HMDB0249986)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 06:57:10 UTC
Update Date2021-09-26 23:01:10 UTC
HMDB IDHMDB0249986
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol
Description(2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms. Based on a literature review a small amount of articles have been published on (2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol. This compound has been identified in human blood as reported by (PMID: 31557052 ). (2r,3r,4r,5s)-2-methyl-tetrahydro-pyran-3,4,5-triol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol 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 HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

  Mrv1652309112108572D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  4  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

HMDB0249986
     RDKit          3D
(2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol
 22 22  0  0  0  0  0  0  0  0999 V2000
   -2.5521   -0.2151   -0.1076 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1102   -0.1179   -0.5888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5827   -1.3874   -0.5679 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7340   -1.4717   -0.9525 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692   -0.7300    0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6070   -1.4724    1.2332 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1212    0.6771    0.2550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8703    1.5210   -0.5940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3372    0.9046    0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9159    1.0777    1.4261 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8532   -1.2724    0.0821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2672    0.1767   -0.8679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6814    0.3003    0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1540    0.1905   -1.6748 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9532   -1.0748   -1.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0185   -2.5413   -0.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6104   -0.7148   -0.3361 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8006   -0.9104    2.0354 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4432    0.9798    1.2949 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6005    2.4652   -0.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4923    1.8981   -0.3600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3819    1.7171    1.9785 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
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
  9 21  1  0
 10 22  1  0
M  END
Download

3D SDF for HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

  Mrv1652309112108572D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  4  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0249986

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1OCC(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O4/c1-3-5(8)6(9)4(7)2-10-3/h3-9H,2H2,1H3

> <INCHI_KEY>
KBVSUNBCTPQWJL-UHFFFAOYSA-N

> <FORMULA>
C6H12O4

> <MOLECULAR_WEIGHT>
148.158

> <EXACT_MASS>
148.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.49302279029428

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyloxane-3,4,5-triol

> <ALOGPS_LOGP>
-2.00

> <JCHEM_LOGP>
-1.521405309666667

> <ALOGPS_LOGS>
0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.700897587891745

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.702581186977156

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5222276685196725

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
33.349799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.89e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
digitoxose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

HMDB0249986
     RDKit          3D
(2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol
 22 22  0  0  0  0  0  0  0  0999 V2000
   -2.5521   -0.2151   -0.1076 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1102   -0.1179   -0.5888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5827   -1.3874   -0.5679 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7340   -1.4717   -0.9525 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692   -0.7300    0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6070   -1.4724    1.2332 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1212    0.6771    0.2550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8703    1.5210   -0.5940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3372    0.9046    0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9159    1.0777    1.4261 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8532   -1.2724    0.0821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2672    0.1767   -0.8679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6814    0.3003    0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1540    0.1905   -1.6748 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9532   -1.0748   -1.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0185   -2.5413   -0.9522 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6104   -0.7148   -0.3361 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8006   -0.9104    2.0354 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4432    0.9798    1.2949 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6005    2.4652   -0.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4923    1.8981   -0.3600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3819    1.7171    1.9785 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
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
  9 21  1  0
 10 22  1  0
M  END
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PDB for HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5                                                            
CONECT    9    4                                                            
CONECT   10    3                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

COMPND    HMDB0249986
HETATM    1  C1  UNL     1      -2.552  -0.215  -0.108  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.110  -0.118  -0.589  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.583  -1.387  -0.568  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.734  -1.472  -0.953  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.569  -0.730   0.057  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.607  -1.472   1.233  1.00  0.00           O  
HETATM    7  C5  UNL     1       1.121   0.677   0.255  1.00  0.00           C  
HETATM    8  O3  UNL     1       1.870   1.521  -0.594  1.00  0.00           O  
HETATM    9  C6  UNL     1      -0.337   0.905   0.156  1.00  0.00           C  
HETATM   10  O4  UNL     1      -0.916   1.078   1.426  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.853  -1.272   0.082  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.267   0.177  -0.868  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.681   0.300   0.880  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.154   0.191  -1.675  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.953  -1.075  -1.952  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.018  -2.541  -0.952  1.00  0.00           H  
HETATM   17  H7  UNL     1       2.610  -0.715  -0.336  1.00  0.00           H  
HETATM   18  H8  UNL     1       1.801  -0.910   2.035  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.443   0.980   1.295  1.00  0.00           H  
HETATM   20  H10 UNL     1       1.601   2.465  -0.444  1.00  0.00           H  
HETATM   21  H11 UNL     1      -0.492   1.898  -0.360  1.00  0.00           H  
HETATM   22  H12 UNL     1      -0.382   1.717   1.979  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    9   14
CONECT    3    4
CONECT    4    5   15   16
CONECT    5    6    7   17
CONECT    6   18
CONECT    7    8    9   19
CONECT    8   20
CONECT    9   10   21
CONECT   10   22
END
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SMILES for HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

CC1OCC(O)C(O)C1O
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INCHI for HMDB0249986 ((2R,3R,4R,5S)-2-Methyl-tetrahydro-pyran-3,4,5-triol)

InChI=1S/C6H12O4/c1-3-5(8)6(9)4(7)2-10-3/h3-9H,2H2,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H12O4
Average Molecular Weight148.158
Monoisotopic Molecular Weight148.073558866
IUPAC Name2-methyloxane-3,4,5-triol
Traditional Namedigitoxose
CAS Registry NumberNot Available
SMILES
CC1OCC(O)C(O)C1O
InChI Identifier
InChI=1S/C6H12O4/c1-3-5(8)6(9)4(7)2-10-3/h3-9H,2H2,1H3
InChI KeyKBVSUNBCTPQWJL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassOxanes
Sub ClassNot Available
Direct ParentOxanes
Alternative Parents
Substituents
  • Oxane
  • Secondary alcohol
  • Oxacycle
  • Polyol
  • Ether
  • Dialkyl ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • 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 ID477149
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound548247
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 ]