Showing metabocard for Coumarin (MMDBc0048296)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 21:55:53 UTC
Update Date2024-09-27 21:34:11 UTC
Metabolite IDMMDBc0048296
Metabolite Identification
Common NameCoumarin
DescriptionCoumarin belongs to the class of chemicals known as chromenones. Specifically it is a chromenone having the keto group located at the 2-position. A chromenone is a benzene molecule with two adjacent hydrogen atoms replaced by a lactone-like chain forming a second six-membered heterocycle that shares two carbons with the benzene ring. Coumarin is also described as a benzopyrone and is considered as a lactone. Coumarin is a colorless crystalline solid with a bitter taste and sweet odor resembling the scent of vanilla or the scent of newly-mowed or recently cut hay. It is a chemical poison found in many plants where it may serve as a chemical defense against predators. Coumarin occurs naturally in many plants and foods such as the tonka bean, woodruff, bison grass, cassia (bastard cinnamon or Chinese cinnamon), cinnamon, melilot (sweet clover), green tea, peppermint, celery, bilberry, lavender, honey (derived both from sweet clover and lavender), and carrots, as well as in beer, tobacco, wine, and other foodstuffs. Coumarin concentrations in these plants, spices, and foods range from <1 mg/kg in celery, to 7000 mg/kg in cinnamon, and up to 87,000 mg/kg in cassia. An estimate of human exposure to coumarin from the diet has been calculated to be 0.02 mg/kg/day. Coumarin is used as an additive in perfumes and fragranced consumer products at concentrations ranging from <0.5% To 6.4% In fine fragrances to <0.01% In detergents. An estimate for systemic exposure of humans from the use of fragranced cosmetic products is 0.04 mg/kg BW/day, assuming complete dermal penetration. The use of coumarin as a food additive was banned by the FDA in 1954 based on reports of hepatotoxicity in rats. It has clinical value as the precursor for several anticoagulants, notably warfarin. Coumarins, as a class, are comprised of numerous naturally occurring benzo-alpha-pyrone compounds with important and diverse physiological activities. Due to its potential hepatotoxic effects in humans, the European Commission restricted coumarin from naturals as a direct food additive to 2 mg/kg food/day, with exceptions granting higher levels for alcoholic beverages, caramel, chewing gum, and certain 'traditional foods'. In addition to human exposure to coumarin from dietary sources and consumer products, coumarin is also used clinically as an antineoplastic and for the treatment of lymphedema and venous insufficiency. Exposure ranges from 11 mg/day for consumption of natural food ingredients to 7 g/day following clinical administration. Although adverse effects in humans following coumarin exposure are rare, and only associated with clinical doses, recent evidence indicates coumarin causes liver tumors in rats and mice and Clara cell toxicity and lung tumors in mice. The multiple effects as well as the ongoing human exposure to coumarin have resulted in a significant research effort focused on understanding the mechanism of coumarin induced toxicity/carcinogenicity and its human relevance. These investigations have revealed significant species differences in coumarin metabolism and toxicity such that the mechanism of coumarin induced effects in rodents, and the relevance of these findings for the safety assessment of coumarin exposure in humans are now better understood. In October 2004, the European Food Safety Authority (EFSA, 2004) reviewed coumarin to establish a tolerable daily intake (TDI) in foods. EFSA issued an opinion indicating that coumarin is not genotoxic, and that a threshold approach to safety assessment was most appropriate. EFSA recommended a TDI of 0 to 0.1 Mg/kg BW/day. Including dietary contributions, the total human exposure is estimated to be 0.06 Mg/kg/day. As a pharmaceutical, coumarin has been used in diverse applications with a wide variety of dosing regimens. Unlike coumadin and other coumarin derivatives, coumarin has no anti-coagulant activity. However, at low doses (typically 7 to 10 mg/day), coumarin has been used as a 'venotonic' to promote vein health and small venule blood flow. Additionally, coumarin has been used clinically in the treatment of high-protein lymphedema arising from various etiologies. (PMID: 16203076 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb0dcf0450>

Coumarin
  Mrv1652309042000192D          

 11 12  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 O   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
    1.4289    0.0000    0.0000 O   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 C   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
    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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  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
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  2 11  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fdb0dcf0450>

HMDB0001218
     RDKit          3D
Coumarin
 17 18  0  0  0  0  0  0  0  0999 V2000
   -3.2947   -1.7915    0.3293 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3110   -1.0135    0.2246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5076    0.3496    0.2055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3916    1.1487    0.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1331    0.5421   -0.0029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0069    1.3085   -0.1207 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2577    0.7316   -0.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3980   -0.6414   -0.1885 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2551   -1.4055   -0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0114   -0.8323    0.0229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0973   -1.5416    0.1346 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4781    0.8141    0.2764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4469    2.2083    0.0657 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9047    2.3933   -0.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1734    1.3371   -0.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3775   -1.1126   -0.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2985   -2.4950   -0.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11  2  1  0
 10  5  1  0
  3 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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3D SDF for #<Metabolite:0x00007fdb0dcf0450>

Coumarin
  Mrv1652309042000192D          

 11 12  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 O   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
    1.4289    0.0000    0.0000 O   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 C   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
    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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  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
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  2 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0048296

> <DATABASE_NAME>
MIME

> <SMILES>
O=C1OC2=CC=CC=C2C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H

> <INCHI_KEY>
ZYGHJZDHTFUPRJ-UHFFFAOYSA-N

> <FORMULA>
C9H6O2

> <MOLECULAR_WEIGHT>
146.145

> <EXACT_MASS>
146.036779433

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
14.362215597078222

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2H-chromen-2-one

> <ALOGPS_LOGP>
1.72

> <JCHEM_LOGP>
1.783359615333333

> <ALOGPS_LOGS>
-2.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.940141845991088

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
41.54860000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
coumarin

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x00007fdb0dcf0450>

HMDB0001218
     RDKit          3D
Coumarin
 17 18  0  0  0  0  0  0  0  0999 V2000
   -3.2947   -1.7915    0.3293 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3110   -1.0135    0.2246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5076    0.3496    0.2055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3916    1.1487    0.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1331    0.5421   -0.0029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0069    1.3085   -0.1207 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2577    0.7316   -0.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3980   -0.6414   -0.1885 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2551   -1.4055   -0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0114   -0.8323    0.0229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0973   -1.5416    0.1346 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4781    0.8141    0.2764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4469    2.2083    0.0657 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9047    2.3933   -0.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1734    1.3371   -0.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3775   -1.1126   -0.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2985   -2.4950   -0.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11  2  1  0
 10  5  1  0
  3 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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PDB for #<Metabolite:0x00007fdb0dcf0450>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Coumarin                                          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10    2                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for #<Metabolite:0x00007fdb0dcf0450>

COMPND    HMDB0001218
HETATM    1  O1  UNL     1      -3.295  -1.791   0.329  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.311  -1.014   0.225  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.508   0.350   0.206  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.392   1.149   0.089  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.133   0.542  -0.003  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.007   1.309  -0.121  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.258   0.732  -0.213  1.00  0.00           C  
HETATM    8  C7  UNL     1       2.398  -0.641  -0.188  1.00  0.00           C  
HETATM    9  C8  UNL     1       1.255  -1.405  -0.070  1.00  0.00           C  
HETATM   10  C9  UNL     1      -0.011  -0.832   0.023  1.00  0.00           C  
HETATM   11  O2  UNL     1      -1.097  -1.542   0.135  1.00  0.00           O  
HETATM   12  H1  UNL     1      -3.478   0.814   0.276  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.447   2.208   0.066  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.905   2.393  -0.140  1.00  0.00           H  
HETATM   15  H4  UNL     1       3.173   1.337  -0.307  1.00  0.00           H  
HETATM   16  H5  UNL     1       3.377  -1.113  -0.260  1.00  0.00           H  
HETATM   17  H6  UNL     1       1.298  -2.495  -0.045  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4    4   12
CONECT    4    5   13
CONECT    5    6    6   10
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   16
CONECT    9   10   10   17
CONECT   10   11
END
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SMILES for #<Metabolite:0x00007fdb0dcf0450>

O=C1OC2=CC=CC=C2C=C1
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INCHI for #<Metabolite:0x00007fdb0dcf0450>

InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H
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Synonyms
ValueSource
1,2-BenzopyroneChEBI
2-Propenoic acid, 3-(2-hydroxyphenyl)-, D-lactoneChEBI
2-Propenoic acid, 3-(2-hydroxyphenyl)-, delta-lactoneChEBI
2H-1-Benzopyran-2-oneChEBI
2H-Benzo[b]pyran-2-oneChEBI
5,6-Benzo-2-pyroneChEBI
Benzo-a-pyroneChEBI
Benzo-alpha-pyroneChEBI
cis-O-Coumarinic acid lactoneChEBI
CoumarineChEBI
Coumarinic anhydrideChEBI
CumarinChEBI
O-Hydroxycinnamic acid delta-lactoneChEBI
O-Hydroxycinnamic acid lactoneChEBI
RattexChEBI
Tonka bean camphorChEBI
Venalot monoKegg
2-Propenoate, 3-(2-hydroxyphenyl)-, D-lactoneGenerator
2-Propenoate, 3-(2-hydroxyphenyl)-, delta-lactoneGenerator
2-Propenoate, 3-(2-hydroxyphenyl)-, δ-lactoneGenerator
2-Propenoic acid, 3-(2-hydroxyphenyl)-, δ-lactoneGenerator
Benzo-α-pyroneGenerator
cis-O-Coumarinate lactoneGenerator
O-Hydroxycinnamate delta-lactoneGenerator
O-Hydroxycinnamate δ-lactoneGenerator
O-Hydroxycinnamic acid δ-lactoneGenerator
O-Hydroxycinnamate lactoneGenerator
5,6-Benzo-alpha-pyroneMeSH
1, 2-BenzopyroneHMDB
2-oxo-1,2-BenzopyranHMDB
2-oxo-2H-1-BenzopyranHMDB
2H-Chromen-2-oneHMDB
2H-Chromen-2-one (acd/name 4.0)HMDB
KumarinHMDB
O-Hydroxycinnamic lactoneHMDB
O-Hydroxyzimtsaure-lactonHMDB
{2h-benzo[b]pyran-2-one}HMDB
Molecular FormulaC9H6O2
Average Mass146.145
Monoisotopic Mass146.036779433
IUPAC Name2H-chromen-2-one
Traditional Namecoumarin
CAS Registry Number91-64-5
SMILES
O=C1OC2=CC=CC=C2C=C1
InChI Identifier
InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H
InChI KeyZYGHJZDHTFUPRJ-UHFFFAOYSA-N