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Showing metabocard for Scopoletin (HMDB0034344)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 19:09:38 UTC
Update Date2023-02-21 17:24:11 UTC
HMDB IDHMDB0034344
Secondary Accession Numbers
  • HMDB34344
Metabolite Identification
Common NameScopoletin
DescriptionScopoletin, also known as 6-methylesculetin, belongs to the class of organic compounds known as 7-hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to the C7 position the coumarin skeleton. Scopoletin exists in all living organisms, ranging from bacteria to humans. Scopoletin is found, on average, in the highest concentration within a few different foods, such as anises (Pimpinella anisum), andean blackberries (Rubus glaucus), and blackberries (Rubus) and in a lower concentration in tropical highland blackberries (Rubus adenotrichos), oats (Avena sativa), and sherry. Scopoletin has also been detected, but not quantified in, several different foods, such as grass peas (Lathyrus sativus), lantern fruits (Physalis alkekengi), pita bread, sweet cherries (Prunus avium), and pepper (capsicum). This could make scopoletin a potential biomarker for the consumption of these foods. Scopoletin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Scopoletin.
Structure
Data?1677000251
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034344 (Scopoletin)

Scopoletin
  Mrv1652309042000382D          

 14 15  0  0  0  0            999 V2000
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   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
    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 O   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    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  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  2  0  0  0  0
  3 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0034344 (Scopoletin)

HMDB0034344
     RDKit          3D
Scopoletin
 22 23  0  0  0  0  0  0  0  0999 V2000
    3.1571    0.3060   -1.4919 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8445    0.1261   -0.1230 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5120    0.0281    0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4952    0.1025   -0.6974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8350    0.0063   -0.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8528    0.0810   -1.2892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1747   -0.0189   -0.9040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4434   -0.1942    0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6675   -0.2815    0.7557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4683   -0.2603    1.3005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1972   -0.1695    0.9739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1794   -0.2423    1.9020 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1549   -0.1475    1.5629 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1650   -0.2267    2.5402 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6115   -0.3810   -2.1527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2444    0.1291   -1.6867 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9827    1.3764   -1.7405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7107    0.2394   -1.7468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6060    0.2181   -2.3295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9468    0.0428   -1.6613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4182   -0.3785    2.9377 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9112   -0.3556    3.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13  3  1  0
 11  5  2  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  4 18  1  0
  6 19  1  0
  7 20  1  0
 12 21  1  0
 14 22  1  0
M  END
Download

3D SDF for HMDB0034344 (Scopoletin)

Scopoletin
  Mrv1652309042000382D          

 14 15  0  0  0  0            999 V2000
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   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
    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 O   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    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  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  2  0  0  0  0
  3 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034344

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C=C2OC(=O)C=CC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H8O4/c1-13-9-4-6-2-3-10(12)14-8(6)5-7(9)11/h2-5,11H,1H3

> <INCHI_KEY>
RODXRVNMMDRFIK-UHFFFAOYSA-N

> <FORMULA>
C10H8O4

> <MOLECULAR_WEIGHT>
192.17

> <EXACT_MASS>
192.042258738

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
18.309998775137817

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-hydroxy-6-methoxy-2H-chromen-2-one

> <ALOGPS_LOGP>
1.65

> <JCHEM_LOGP>
1.3221230279999998

> <ALOGPS_LOGS>
-1.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.263751612912468

> <JCHEM_PKA_STRONGEST_BASIC>
-4.882342454181455

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
49.99270000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.35e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
scopoletin

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0034344 (Scopoletin)

HMDB0034344
     RDKit          3D
Scopoletin
 22 23  0  0  0  0  0  0  0  0999 V2000
    3.1571    0.3060   -1.4919 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8445    0.1261   -0.1230 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5120    0.0281    0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4952    0.1025   -0.6974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8350    0.0063   -0.3458 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8528    0.0810   -1.2892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1747   -0.0189   -0.9040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4434   -0.1942    0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6675   -0.2815    0.7557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4683   -0.2603    1.3005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1972   -0.1695    0.9739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1794   -0.2423    1.9020 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1549   -0.1475    1.5629 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1650   -0.2267    2.5402 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6115   -0.3810   -2.1527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2444    0.1291   -1.6867 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9827    1.3764   -1.7405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7107    0.2394   -1.7468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6060    0.2181   -2.3295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9468    0.0428   -1.6613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4182   -0.3785    2.9377 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9112   -0.3556    3.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13  3  1  0
 11  5  2  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  4 18  1  0
  6 19  1  0
  7 20  1  0
 12 21  1  0
 14 22  1  0
M  END
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PDB for HMDB0034344 (Scopoletin)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Scopoletin                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000  -3.080   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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    7   14                                                  
CONECT   14   13    3                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END
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3D PDB for HMDB0034344 (Scopoletin)

COMPND    HMDB0034344
HETATM    1  C1  UNL     1       3.157   0.306  -1.492  1.00  0.00           C  
HETATM    2  O1  UNL     1       2.845   0.126  -0.123  1.00  0.00           O  
HETATM    3  C2  UNL     1       1.512   0.028   0.243  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.495   0.102  -0.697  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.835   0.006  -0.346  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.853   0.081  -1.289  1.00  0.00           C  
HETATM    7  C6  UNL     1      -3.175  -0.019  -0.904  1.00  0.00           C  
HETATM    8  C7  UNL     1      -3.443  -0.194   0.442  1.00  0.00           C  
HETATM    9  O2  UNL     1      -4.668  -0.282   0.756  1.00  0.00           O  
HETATM   10  O3  UNL     1      -2.468  -0.260   1.300  1.00  0.00           O  
HETATM   11  C8  UNL     1      -1.197  -0.170   0.974  1.00  0.00           C  
HETATM   12  C9  UNL     1      -0.179  -0.242   1.902  1.00  0.00           C  
HETATM   13  C10 UNL     1       1.155  -0.148   1.563  1.00  0.00           C  
HETATM   14  O4  UNL     1       2.165  -0.227   2.540  1.00  0.00           O  
HETATM   15  H1  UNL     1       2.611  -0.381  -2.153  1.00  0.00           H  
HETATM   16  H2  UNL     1       4.244   0.129  -1.687  1.00  0.00           H  
HETATM   17  H3  UNL     1       2.983   1.376  -1.740  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.711   0.239  -1.747  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.606   0.218  -2.330  1.00  0.00           H  
HETATM   20  H6  UNL     1      -3.947   0.043  -1.661  1.00  0.00           H  
HETATM   21  H7  UNL     1      -0.418  -0.379   2.938  1.00  0.00           H  
HETATM   22  H8  UNL     1       1.911  -0.356   3.511  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3
CONECT    3    4    4   13
CONECT    4    5   18
CONECT    5    6   11   11
CONECT    6    7    7   19
CONECT    7    8   20
CONECT    8    9    9   10
CONECT   10   11
CONECT   11   12
CONECT   12   13   13   21
CONECT   13   14
CONECT   14   22
END
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SMILES for HMDB0034344 (Scopoletin)

COC1=C(O)C=C2OC(=O)C=CC2=C1
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INCHI for HMDB0034344 (Scopoletin)

InChI=1S/C10H8O4/c1-13-9-4-6-2-3-10(12)14-8(6)5-7(9)11/h2-5,11H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC10H8O4
Average Molecular Weight192.17
Monoisotopic Molecular Weight192.042258738
IUPAC Name7-hydroxy-6-methoxy-2H-chromen-2-one
Traditional Namescopoletin
CAS Registry Number92-61-5
SMILES
COC1=C(O)C=C2OC(=O)C=CC2=C1
InChI Identifier
InChI=1S/C10H8O4/c1-13-9-4-6-2-3-10(12)14-8(6)5-7(9)11/h2-5,11H,1H3
InChI KeyRODXRVNMMDRFIK-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 7-hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to the C7 position the coumarin skeleton.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCoumarins and derivatives
Sub ClassHydroxycoumarins
Direct Parent7-hydroxycoumarins
Alternative Parents
Substituents
  • 7-hydroxycoumarin
  • Benzopyran
  • 1-benzopyran
  • Anisole
  • 1-hydroxy-2-unsubstituted benzenoid
  • Alkyl aryl ether
  • Pyranone
  • Pyran
  • Benzenoid
  • Heteroaromatic compound
  • Lactone
  • Oxacycle
  • Ether
  • Organoheterocyclic compound
  • Organic oxygen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point204 °CNot Available
Boiling Point410.80 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-1.880 (est)The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available133.603http://allccs.zhulab.cn/database/detail?ID=AllCCS00001473
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 ID638
FooDB IDFDB012705
KNApSAcK IDC00002499
Chemspider ID4444113
KEGG Compound IDC01752
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkScopoletin
METLIN IDNot Available
PubChem Compound5280460
PDB IDNot Available
ChEBI ID17488
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1495271
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details
1. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
Scopoletin → 3,4,5-trihydroxy-6-[(6-methoxy-2-oxo-2H-chromen-7-yl)oxy]oxane-2-carboxylic aciddetails