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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 07:31:41 UTC

Update Date

2021-09-26 23:01:58 UTC

HMDB ID

HMDB0250498

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Coumestan

Description

Coumestan belongs to the class of organic compounds known as coumestans. These are polycyclic aromatic compounds containing a coumestan moiety, which consists of a benzoxole fused to a chromen-2-one to form 1-Benzoxolo[3,2-c]chromen-6-one. They are oxidation products of pterocarpan. Coumestan 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 Coumestan. This compound has been identified in human blood as reported by (PMID: 31557052 ). Coumestan is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Coumestan 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309112109312D          

 18 21  0  0  0  0            999 V2000
    5.0376    0.8585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0768    0.0344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3828   -0.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6495   -0.0335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6103    0.7906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3043    1.2366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8144    1.0079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3618    0.3182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8779   -0.3254    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5381    0.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0855   -0.3244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2618   -0.2772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1092    0.4596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3435    1.1494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1671    1.1022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6198    1.7920    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4434    1.7448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8961    2.4345    0.0000 O   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  7 17  1  0  0  0  0
 17 18  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250498

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1OC2=CC=CC=C2C2=C1C1=CC=CC=C1O2

> <INCHI_IDENTIFIER>
InChI=1S/C15H8O3/c16-15-13-9-5-1-3-7-11(9)17-14(13)10-6-2-4-8-12(10)18-15/h1-8H

> <INCHI_KEY>
JBIZUYWOIKFETJ-UHFFFAOYSA-N

> <FORMULA>
C15H8O3

> <MOLECULAR_WEIGHT>
236.226

> <EXACT_MASS>
236.047344118

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
24.20864114192806

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,11,13,15-heptaen-9-one

> <ALOGPS_LOGP>
3.21

> <JCHEM_LOGP>
3.004451965666666

> <ALOGPS_LOGS>
-3.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1209148631476933

> <JCHEM_POLAR_SURFACE_AREA>
39.44

> <JCHEM_REFRACTIVITY>
65.65770000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.52e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,11,13,15-heptaen-9-one

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       9.404   1.603   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.477   0.064   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.181  -0.768   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.812  -0.063   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.739   1.476   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.035   2.308   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.254   1.881   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.409   0.594   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.372  -0.607   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.871   0.682   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.026  -0.606   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.489  -0.517   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.204   0.858   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.641   2.146   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.179   2.057   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.024   3.345   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.561   3.257   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.406   4.544   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   17                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16    7   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   42    0
END

COMPND    HMDB0250498
HETATM    1  O1  UNL     1       0.361  -3.063   0.078  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.276  -1.978   0.028  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.595  -1.969  -0.047  1.00  0.00           O  
HETATM    4  C2  UNL     1      -2.282  -0.846  -0.101  1.00  0.00           C  
HETATM    5  C3  UNL     1      -3.661  -0.854  -0.180  1.00  0.00           C  
HETATM    6  C4  UNL     1      -4.416   0.299  -0.238  1.00  0.00           C  
HETATM    7  C5  UNL     1      -3.717   1.501  -0.215  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.339   1.530  -0.137  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.602   0.360  -0.079  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.225   0.379  -0.001  1.00  0.00           C  
HETATM   11  O3  UNL     1       0.623   1.355   0.034  1.00  0.00           O  
HETATM   12  C9  UNL     1       1.862   0.881   0.110  1.00  0.00           C  
HETATM   13  C10 UNL     1       3.110   1.448   0.174  1.00  0.00           C  
HETATM   14  C11 UNL     1       4.279   0.707   0.250  1.00  0.00           C  
HETATM   15  C12 UNL     1       4.161  -0.666   0.262  1.00  0.00           C  
HETATM   16  C13 UNL     1       2.922  -1.271   0.200  1.00  0.00           C  
HETATM   17  C14 UNL     1       1.789  -0.497   0.125  1.00  0.00           C  
HETATM   18  C15 UNL     1       0.448  -0.811   0.053  1.00  0.00           C  
HETATM   19  H1  UNL     1      -4.193  -1.791  -0.197  1.00  0.00           H  
HETATM   20  H2  UNL     1      -5.501   0.280  -0.299  1.00  0.00           H  
HETATM   21  H3  UNL     1      -4.250   2.454  -0.258  1.00  0.00           H  
HETATM   22  H4  UNL     1      -1.829   2.484  -0.121  1.00  0.00           H  
HETATM   23  H5  UNL     1       3.185   2.523   0.163  1.00  0.00           H  
HETATM   24  H6  UNL     1       5.260   1.173   0.299  1.00  0.00           H  
HETATM   25  H7  UNL     1       5.050  -1.278   0.320  1.00  0.00           H  
HETATM   26  H8  UNL     1       2.835  -2.351   0.209  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   18
CONECT    3    4
CONECT    4    5    5    9
CONECT    5    6   19
CONECT    6    7    7   20
CONECT    7    8   21
CONECT    8    9    9   22
CONECT    9   10
CONECT   10   11   18   18
CONECT   11   12
CONECT   12   13   13   17
CONECT   13   14   23
CONECT   14   15   15   24
CONECT   15   16   25
CONECT   16   17   17   26
CONECT   17   18
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
6H-Benzofuro(3,2-c)(1)benzopyran-6-one	ChEBI
Benzofurano(3',2':3,4)coumarin	ChEBI
(1)Benzoxolo(3,2-c)chromen-6-one	HMDB

Chemical Formula

C₁₅H₈O₃

Average Molecular Weight

236.226

Monoisotopic Molecular Weight

236.047344118

IUPAC Name

8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,11,13,15-heptaen-9-one

Traditional Name

8,17-dioxatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,11,13,15-heptaen-9-one

CAS Registry Number

Not Available

SMILES

O=C1OC2=CC=CC=C2C2=C1C1=CC=CC=C1O2

InChI Identifier

InChI=1S/C15H8O3/c16-15-13-9-5-1-3-7-11(9)17-14(13)10-6-2-4-8-12(10)18-15/h1-8H

InChI Key

JBIZUYWOIKFETJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumestans. These are polycyclic aromatic compounds containing a coumestan moiety, which consists of a benzoxole fused to a chromen-2-one to form 1-Benzoxolo[3,2-c]chromen-6-one. They are oxidation products of pterocarpan.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Coumestans

Direct Parent

Coumestans

Alternative Parents

Substituents

Coumestan
Angular furanocoumarin
Furanocoumarin
Coumarin
Benzopyran
1-benzopyran
Benzofuran
Furopyran
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Furan
Lactone
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

delta-lactone (CHEBI:72578 )
coumestans (CHEBI:72578 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.21	ALOGPS
logP	3	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	39.44 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	65.66 m³·mol⁻¹	ChemAxon
Polarizability	24.21 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	148.6	30932474
DeepCCS	[M-H]-	146.204	30932474
DeepCCS	[M-2H]-	179.843	30932474
DeepCCS	[M+Na]+	154.553	30932474
AllCCS	[M+H]+	151.3	32859911
AllCCS	[M+H-H2O]+	147.0	32859911
AllCCS	[M+NH4]+	155.2	32859911
AllCCS	[M+Na]+	156.4	32859911
AllCCS	[M-H]-	153.9	32859911
AllCCS	[M+Na-2H]-	152.7	32859911
AllCCS	[M+HCOO]-	151.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	18.0266 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.43 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2872.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	690.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	272.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	455.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	374.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	636.5 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	711.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	261.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1583.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	611.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1533.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	538.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	422.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	533.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	411.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	28.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Coumestan	O=C1OC2=CC=CC=C2C2=C1C1=CC=CC=C1O2	3353.7	Standard polar	33892256
Coumestan	O=C1OC2=CC=CC=C2C2=C1C1=CC=CC=C1O2	2233.4	Standard non polar	33892256
Coumestan	O=C1OC2=CC=CC=C2C2=C1C1=CC=CC=C1O2	2306.3	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Coumestan GC-MS (Non-derivatized) - 70eV, Positive	splash10-000i-0090000000-34026e6b1696ee1c652e	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Coumestan GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Coumestan 10V, Positive-QTOF	splash10-000i-0090000000-2416cb512b621fff5992	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Coumestan 20V, Positive-QTOF	splash10-000i-0090000000-2416cb512b621fff5992	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Coumestan 40V, Positive-QTOF	splash10-000i-0090000000-2416cb512b621fff5992	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Coumestan 10V, Negative-QTOF	splash10-000i-0090000000-90c010ef68ab39873860	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Coumestan 20V, Negative-QTOF	splash10-000i-0090000000-90c010ef68ab39873860	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Coumestan 40V, Negative-QTOF	splash10-052r-0090000000-b69c35954d6c9d68dbe8	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00002514

Chemspider ID

553855

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Coumestan

METLIN ID

Not Available

PubChem Compound

638309

PDB ID

Not Available

ChEBI ID

72578

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Coumestan (HMDB0250498)

MOL for HMDB0250498 (Coumestan)

3D MOL for HMDB0250498 (Coumestan)

3D SDF for HMDB0250498 (Coumestan)

3D-SDF for HMDB0250498 (Coumestan)

PDB for HMDB0250498 (Coumestan)

3D PDB for HMDB0250498 (Coumestan)

SMILES for HMDB0250498 (Coumestan)

INCHI for HMDB0250498 (Coumestan)

Structure for HMDB0250498 (Coumestan)

3D Structure for HMDB0250498 (Coumestan)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra