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Showing metabocard for Lichenin (HMDB0302349)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:06:11 UTC
Update Date2021-09-23 17:06:11 UTC
HMDB IDHMDB0302349
Secondary Accession NumbersNone
Metabolite Identification
Common NameLichenin
DescriptionLichenin, also known as lichenan or moss starch, is a complex glucan occurring in certain species of lichens. It can be extracted from Cetraria islandica (Iceland moss). It has been studied since about 1957. Chemically, lichenin consists of repeating glucose units linked by beta-1,3 and beta-1,4 glycosidic bonds . Lichenin is soluble (in water) and a very weakly acidic compound (based on its pKa). Lichenin can be found in oat, which makes lichenin a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302349 (Lichenin)


  Mrv0541 02241221222D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  2  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
  3  2  1  1  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  2  0  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  5 10  1  1  0  0  0
  4 11  1  6  0  0  0
M  END
Download

3D MOL for HMDB0302349 (Lichenin)

HMDB0302349
     RDKit          3D
Lichenin
 21 21  0  0  0  0  0  0  0  0999 V2000
    3.0839    0.0184    0.2891 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8762    0.4404   -0.2876 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7983   -0.2795    0.1816 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2248   -0.9986   -0.8930 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1488   -1.0853   -1.0859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8857   -0.0355   -0.7503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2628   -0.0510   -0.9151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1583    1.1389   -0.1963 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3723    1.7429   -1.1985 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2142    0.6085    0.8619 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9710   -0.1401    1.7908 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2499   -1.0421    0.0523 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8847    0.6914   -0.0829 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0770    0.1392    1.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1390   -1.0454    0.9248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6327   -1.9580   -1.4911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8844    0.0663   -0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.8993    0.2065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7397    1.5983   -2.0892 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2219    1.4635    1.3771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4452   -0.9661    2.0216 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  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  3  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  1
  5 16  1  0
  7 17  1  0
  8 18  1  1
  9 19  1  0
 10 20  1  1
 11 21  1  0
M  END
Download

3D SDF for HMDB0302349 (Lichenin)


  Mrv0541 02241221222D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  2  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
  3  2  1  1  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  2  0  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  5 10  1  1  0  0  0
  4 11  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0302349

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c1-10-6-5(9)4(8)3(7)2-11-6/h2,4-9H,1H3/t4-,5+,6+/m0/s1

> <INCHI_KEY>
FSOIXBFBUZWTMV-KVQBGUIXSA-N

> <FORMULA>
C6H10O5

> <MOLECULAR_WEIGHT>
162.1406

> <EXACT_MASS>
162.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.40973164639069

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-2-methoxy-3,4-dihydro-2H-pyran-3,4,5-triol

> <ALOGPS_LOGP>
-1.52

> <JCHEM_LOGP>
-1.3989494793333328

> <ALOGPS_LOGS>
0.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.511990706111959

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.03914374238929

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7979338069000823

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
35.489999999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.17e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R)-2-methoxy-3,4-dihydro-2H-pyran-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0302349 (Lichenin)

HMDB0302349
     RDKit          3D
Lichenin
 21 21  0  0  0  0  0  0  0  0999 V2000
    3.0839    0.0184    0.2891 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8762    0.4404   -0.2876 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7983   -0.2795    0.1816 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2248   -0.9986   -0.8930 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1488   -1.0853   -1.0859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8857   -0.0355   -0.7503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2628   -0.0510   -0.9151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1583    1.1389   -0.1963 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3723    1.7429   -1.1985 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2142    0.6085    0.8619 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9710   -0.1401    1.7908 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2499   -1.0421    0.0523 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8847    0.6914   -0.0829 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0770    0.1392    1.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1390   -1.0454    0.9248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6327   -1.9580   -1.4911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8844    0.0663   -0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.8993    0.2065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7397    1.5983   -2.0892 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2219    1.4635    1.3771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4452   -0.9661    2.0216 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  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  3  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  1
  5 16  1  0
  7 17  1  0
  8 18  1  1
  9 19  1  0
 10 20  1  1
 11 21  1  0
M  END
Download

PDB for HMDB0302349 (Lichenin)

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       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    6                                                            
CONECT   10    5                                                            
CONECT   11    4                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for HMDB0302349 (Lichenin)

COMPND    HMDB0302349
HETATM    1  C1  UNL     1       3.084   0.018   0.289  1.00  0.00           C  
HETATM    2  O1  UNL     1       1.876   0.440  -0.288  1.00  0.00           O  
HETATM    3  C2  UNL     1       0.798  -0.279   0.182  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.225  -0.999  -0.893  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.149  -1.085  -1.086  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.886  -0.035  -0.750  1.00  0.00           C  
HETATM    7  O3  UNL     1      -3.263  -0.051  -0.915  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.158   1.139  -0.196  1.00  0.00           C  
HETATM    9  O4  UNL     1      -0.372   1.743  -1.198  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.214   0.608   0.862  1.00  0.00           C  
HETATM   11  O5  UNL     1      -0.971  -0.140   1.791  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.250  -1.042   0.052  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.885   0.691  -0.083  1.00  0.00           H  
HETATM   14  H3  UNL     1       3.077   0.139   1.395  1.00  0.00           H  
HETATM   15  H4  UNL     1       1.139  -1.045   0.925  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.633  -1.958  -1.491  1.00  0.00           H  
HETATM   17  H6  UNL     1      -3.884   0.066  -0.111  1.00  0.00           H  
HETATM   18  H7  UNL     1      -1.840   1.899   0.206  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.740   1.598  -2.089  1.00  0.00           H  
HETATM   20  H9  UNL     1       0.222   1.463   1.377  1.00  0.00           H  
HETATM   21  H10 UNL     1      -0.445  -0.966   2.022  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3
CONECT    3    4   10   15
CONECT    4    5
CONECT    5    6    6   16
CONECT    6    7    8
CONECT    7   17
CONECT    8    9   10   18
CONECT    9   19
CONECT   10   11   20
CONECT   11   21
END
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SMILES for HMDB0302349 (Lichenin)

CO[C@@H]1OC=C(O)[C@H](O)[C@H]1O
Download

INCHI for HMDB0302349 (Lichenin)

InChI=1S/C6H10O5/c1-10-6-5(9)4(8)3(7)2-11-6/h2,4-9H,1H3/t4-,5+,6+/m0/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H10O5
Average Molecular Weight162.1406
Monoisotopic Molecular Weight162.05282343
IUPAC Name(2R,3R,4R)-2-methoxy-3,4-dihydro-2H-pyran-3,4,5-triol
Traditional Name(2R,3R,4R)-2-methoxy-3,4-dihydro-2H-pyran-3,4,5-triol
CAS Registry NumberNot Available
SMILES
CO[C@@H]1OC=C(O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C6H10O5/c1-10-6-5(9)4(8)3(7)2-11-6/h2,4-9H,1H3/t4-,5+,6+/m0/s1
InChI KeyFSOIXBFBUZWTMV-KVQBGUIXSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct Parent1,2-diols
Alternative Parents
Substituents
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Acetal
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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
PropertyValueSource
logP-1.5ALOGPS
logP-1.4ChemAxon
logS0.58ALOGPS
pKa (Strongest Acidic)6.04ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area79.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.49 m³·mol⁻¹ChemAxon
Polarizability14.41 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+136.62432859911
AllCCS[M+H-H2O]+132.17532859911
AllCCS[M+Na]+141.96932859911
AllCCS[M+NH4]+140.77232859911
AllCCS[M-H]-129.57432859911
AllCCS[M+Na-2H]-130.96432859911
AllCCS[M+HCOO]-132.55132859911
DeepCCS[M+H]+136.86930932474
DeepCCS[M-H]-134.55230932474
DeepCCS[M-2H]-169.02530932474
DeepCCS[M+Na]+143.44830932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 10V, Positive-QTOFsplash10-03di-0900000000-5b2cab6c33b2027bbfb42016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 20V, Positive-QTOFsplash10-03dj-1900000000-ec4cb6eb1770d39b80ab2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 40V, Positive-QTOFsplash10-074l-9300000000-2845fccadce241ec7a0c2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 10V, Negative-QTOFsplash10-03di-2900000000-63b285c9c8de1149e7332016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 20V, Negative-QTOFsplash10-03dl-4900000000-e0ad1474087f8814cd882016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 40V, Negative-QTOFsplash10-0006-9000000000-aed38348aefbf8bca0962016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 10V, Positive-QTOFsplash10-01q9-0900000000-70e8c421e393ac6650c82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 20V, Positive-QTOFsplash10-0h36-9700000000-b8123846c38bf027a4ad2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 40V, Positive-QTOFsplash10-052e-9000000000-ca13b71f1f8df4de70f92021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 10V, Negative-QTOFsplash10-03fr-1900000000-d6ad3751f425602d93782021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 20V, Negative-QTOFsplash10-0a6r-9500000000-f88f6f3303c49190c5802021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lichenin 40V, Negative-QTOFsplash10-0a4i-9100000000-07065ff5d611f556c6d72021-10-21Wishart LabView Spectrum
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 IDFDB004232
KNApSAcK IDNot Available
Chemspider ID59696320
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44149648
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