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Showing metabocard for isosorbide (HMDB0253693)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 12:30:16 UTC
Update Date2021-09-26 23:07:05 UTC
HMDB IDHMDB0253693
Secondary Accession NumbersNone
Metabolite Identification
Common Nameisosorbide
DescriptionIsomannide belongs to the class of organic compounds known as isosorbides. These are organic polycyclic compounds containing an isosorbide(1,4-Dianhydrosorbitol) moiety, which consists of two -oxolan-3-ol rings. Isomannide is an extremely weak basic (essentially neutral) compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Isosorbide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically isosorbide 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 HMDB0253693 (isosorbide)


  Mrv1533004161509442D          

 10 11  0  0  0  0            999 V2000
    1.0146   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937    1.1971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    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
  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
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  2 10  1  0  0  0  0
  5 10  1  0  0  0  0
M  END
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3D MOL for HMDB0253693 (isosorbide)

HMDB0253693
     RDKit          3D
isosorbide
 20 21  0  0  0  0  0  0  0  0999 V2000
   -2.7175   -0.9789   -0.2164 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5675   -0.3723   -0.7122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6688    1.1520   -0.6486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2958    1.4876   -0.6845 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1609    0.7529    0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6348    0.4917    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1780    0.8415   -0.8627 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6828   -1.0341    0.4721 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6069   -1.3673   -0.3792 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4253   -0.6350    0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4786   -1.8355    0.2442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2899   -0.7088   -1.7189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2213    1.5696   -1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0479    1.4445    0.3413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813    1.2336    1.3514 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1708    0.9348    1.2255 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1662    0.9077   -0.7456 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6326   -1.4459    0.1311 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3859   -1.3872    1.4780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7251   -1.0508    1.1975 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  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10  2  1  0
 10  5  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
 10 20  1  0
M  END
Download

3D SDF for HMDB0253693 (isosorbide)


  Mrv1533004161509442D          

 10 11  0  0  0  0            999 V2000
    1.0146   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937    1.1971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    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
  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
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  2 10  1  0  0  0  0
  5 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253693

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1COC2C(O)COC12

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O4/c7-3-1-9-6-4(8)2-10-5(3)6/h3-8H,1-2H2

> <INCHI_KEY>
KLDXJTOLSGUMSJ-UHFFFAOYSA-N

> <FORMULA>
C6H10O4

> <MOLECULAR_WEIGHT>
146.142

> <EXACT_MASS>
146.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.520532099954057

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
hexahydrofuro[3,2-b]furan-3,6-diol

> <ALOGPS_LOGP>
-1.50

> <JCHEM_LOGP>
-1.406611704

> <ALOGPS_LOGS>
0.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.643410080149245

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.034376302842013

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526893285033477

> <JCHEM_POLAR_SURFACE_AREA>
58.92

> <JCHEM_REFRACTIVITY>
31.383399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.21e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isosorbide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0253693 (isosorbide)

HMDB0253693
     RDKit          3D
isosorbide
 20 21  0  0  0  0  0  0  0  0999 V2000
   -2.7175   -0.9789   -0.2164 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5675   -0.3723   -0.7122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6688    1.1520   -0.6486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2958    1.4876   -0.6845 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1609    0.7529    0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6348    0.4917    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1780    0.8415   -0.8627 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6828   -1.0341    0.4721 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6069   -1.3673   -0.3792 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4253   -0.6350    0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4786   -1.8355    0.2442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2899   -0.7088   -1.7189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2213    1.5696   -1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0479    1.4445    0.3413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813    1.2336    1.3514 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1708    0.9348    1.2255 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1662    0.9077   -0.7456 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6326   -1.4459    0.1311 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3859   -1.3872    1.4780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7251   -1.0508    1.1975 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  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10  2  1  0
 10  5  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
 10 20  1  0
M  END
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PDB for HMDB0253693 (isosorbide)

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0       1.894  -3.186   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.370   0.770   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.834   0.294   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.775   2.235   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.299  -1.722   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    2    5                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0253693 (isosorbide)

COMPND    HMDB0253693
HETATM    1  O1  UNL     1      -2.718  -0.979  -0.216  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.568  -0.372  -0.712  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.669   1.152  -0.649  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.296   1.488  -0.684  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.161   0.753   0.423  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.635   0.492   0.372  1.00  0.00           C  
HETATM    7  O3  UNL     1       2.178   0.841  -0.863  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.683  -1.034   0.472  1.00  0.00           C  
HETATM    9  O4  UNL     1       0.607  -1.367  -0.379  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.425  -0.635   0.227  1.00  0.00           C  
HETATM   11  H1  UNL     1      -2.479  -1.836   0.244  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.290  -0.709  -1.719  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.221   1.570  -1.495  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.048   1.444   0.341  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.181   1.234   1.351  1.00  0.00           H  
HETATM   16  H6  UNL     1       2.171   0.935   1.226  1.00  0.00           H  
HETATM   17  H7  UNL     1       3.166   0.908  -0.746  1.00  0.00           H  
HETATM   18  H8  UNL     1       2.633  -1.446   0.131  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.386  -1.387   1.478  1.00  0.00           H  
HETATM   20  H10 UNL     1      -0.725  -1.051   1.198  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   10   12
CONECT    3    4   13   14
CONECT    4    5
CONECT    5    6   10   15
CONECT    6    7    8   16
CONECT    7   17
CONECT    8    9   18   19
CONECT    9   10
CONECT   10   20
END
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SMILES for HMDB0253693 (isosorbide)

OC1COC2C(O)COC12
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INCHI for HMDB0253693 (isosorbide)

InChI=1S/C6H10O4/c7-3-1-9-6-4(8)2-10-5(3)6/h3-8H,1-2H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,4-3,6-Dianhydro-D-mannitolMeSH
Chemical FormulaC6H10O4
Average Molecular Weight146.142
Monoisotopic Molecular Weight146.057908802
IUPAC Namehexahydrofuro[3,2-b]furan-3,6-diol
Traditional Nameisosorbide
CAS Registry NumberNot Available
SMILES
OC1COC2C(O)COC12
InChI Identifier
InChI=1S/C6H10O4/c7-3-1-9-6-4(8)2-10-5(3)6/h3-8H,1-2H2
InChI KeyKLDXJTOLSGUMSJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isosorbides. These are organic polycyclic compounds containing an isosorbide(1,4-Dianhydrosorbitol) moiety, which consists of two -oxolan-3-ol rings.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassFurofurans
Sub ClassIsosorbides
Direct ParentIsosorbides
Alternative Parents
Substituents
  • Isosorbide
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Ether
  • Dialkyl ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic 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
PropertyValueSource
logP-1.5ALOGPS
logP-1.4ChemAxon
logS0.92ALOGPS
pKa (Strongest Acidic)13.03ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.92 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity31.38 m³·mol⁻¹ChemAxon
Polarizability13.52 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-161.74930932474
DeepCCS[M+Na]+136.54130932474
AllCCS[M+H]+132.932859911
AllCCS[M+H-H2O]+128.232859911
AllCCS[M+NH4]+137.332859911
AllCCS[M+Na]+138.632859911
AllCCS[M-H]-126.932859911
AllCCS[M+Na-2H]-128.132859911
AllCCS[M+HCOO]-129.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.8722 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.51 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid888.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid294.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid60.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid182.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid50.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid260.2 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid262.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)546.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid586.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid54.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid840.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid192.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid177.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate537.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA272.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water260.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
isosorbideOC1COC2C(O)COC122553.9Standard polar33892256
isosorbideOC1COC2C(O)COC121224.8Standard non polar33892256
isosorbideOC1COC2C(O)COC121432.8Semi standard non polar33892256
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 Compound99937
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 ]