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Showing metabocard for Coumarin (HMDB0001218)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:32 UTC
HMDB IDHMDB0001218
Secondary Accession Numbers
  • HMDB01218
Metabolite Identification
Common NameCoumarin
Description
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001218 (Coumarin)

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
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3D MOL for HMDB0001218 (Coumarin)

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 HMDB0001218 (Coumarin)

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>
HMDB0001218

> <DATABASE_NAME>
hmdb

> <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 HMDB0001218 (Coumarin)

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 HMDB0001218 (Coumarin)

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 HMDB0001218 (Coumarin)

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 HMDB0001218 (Coumarin)

O=C1OC2=CC=CC=C2C=C1
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INCHI for HMDB0001218 (Coumarin)

InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC9H6O2
Average Molecular Weight146.145
Monoisotopic Molecular Weight146.036779433
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
Chemical Taxonomy
Description Belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one).
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCoumarins and derivatives
Sub ClassNot Available
Direct ParentCoumarins and derivatives
Alternative Parents
Substituents
  • Coumarin
  • 1-benzopyran
  • Benzopyran
  • Pyranone
  • Benzenoid
  • Pyran
  • Heteroaromatic compound
  • Lactone
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point71 °CNot Available
Boiling Point297.00 to 301.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1.9 mg/mLNot Available
LogP2.23Not Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available122.248http://allccs.zhulab.cn/database/detail?ID=AllCCS00001384
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB04665
Phenol Explorer Compound ID635
FooDB IDFDB011938
KNApSAcK IDC00002460
Chemspider ID13848793
KEGG Compound IDC05851
BioCyc IDCOUMARIN
BiGG ID46647
Wikipedia LinkCoumarin
METLIN ID3525
PubChem Compound323
PDB IDNot Available
ChEBI ID28794
Food Biomarker OntologyNot Available
VMH IDCOUMARIN
MarkerDB IDNot Available
Good Scents IDrw1003832
References
Synthesis ReferenceHuang, Zhong-jing. Synthesis of coumarin under microwave irradiation. Guangxi Huagong (2001), 30(3), 1-2.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Felter SP, Vassallo JD, Carlton BD, Daston GP: A safety assessment of coumarin taking into account species-specificity of toxicokinetics. Food Chem Toxicol. 2006 Apr;44(4):462-75. Epub 2005 Oct 3. [PubMed:16203076 ]

Enzymes

Enzyme Details
1. Cytochrome P450 2A13
General function:
Involved in monooxygenase activity
Specific function:
Exhibits a coumarin 7-hydroxylase activity. Active in the metabolic activation of hexamethylphosphoramide, N,N-dimethylaniline, 2'-methoxyacetophenone, N-nitrosomethylphenylamine, and the tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Possesses phenacetin O-deethylation activity.
Gene Name:
CYP2A13
Uniprot ID:
Q16696
Molecular weight:
56687.095
Enzyme Details
2. Cytochrome P450 2A6
General function:
Involved in monooxygenase activity
Specific function:
Exhibits a high coumarin 7-hydroxylase activity. Can act in the hydroxylation of the anti-cancer drugs cyclophosphamide and ifosphamide. Competent in the metabolic activation of aflatoxin B1. Constitutes the major nicotine C-oxidase. Acts as a 1,4-cineole 2-exo-monooxygenase. Possesses low phenacetin O-deethylation activity.
Gene Name:
CYP2A6
Uniprot ID:
P11509
Molecular weight:
56517.005