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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2006-05-22 14:17:38 UTC

Update Date

2023-02-21 17:16:13 UTC

HMDB ID

HMDB0002149

Secondary Accession Numbers

HMDB02149

Metabolite Identification

Common Name

3 Hydroxycoumarin

Description

3 Hydroxycoumarin belongs to the class of organic compounds known as hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to the coumarin skeleton. 3 Hydroxycoumarin has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3 hydroxycoumarin a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 3 Hydroxycoumarin.

Structure

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

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      43.444 -21.358   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      40.831 -24.375   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      40.831 -21.358   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      44.750 -23.621   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      44.750 -22.112   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      43.444 -24.375   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      46.099 -24.427   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      46.099 -21.305   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      42.137 -23.621   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      47.466 -23.652   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      47.466 -22.081   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      42.137 -22.112   0.000  0.00  0.00           C+0
CONECT    1    5   12                                                       
CONECT    2    9                                                            
CONECT    3   12                                                            
CONECT    4    5    6    7                                                  
CONECT    5    1    4    8                                                  
CONECT    6    4    9                                                       
CONECT    7    4   10                                                       
CONECT    8    5   11                                                       
CONECT    9    2    6   12                                                  
CONECT   10    7   11                                                       
CONECT   11    8   10                                                       
CONECT   12    1    3    9                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-Hydroxy-2-benzopyrone	HMDB
3-Hydroxy-2H-1-benzopyran-2-one	HMDB
3-Hydroxy-coumarin	HMDB
3-Hydroxycoumarin	HMDB, MeSH
O-Hydroxyphenylpyruvic acid lactone	HMDB

Chemical Formula

C₉H₆O₃

Average Molecular Weight

162.1421

Monoisotopic Molecular Weight

162.031694058

IUPAC Name

3-hydroxy-2H-chromen-2-one

Traditional Name

3 hydroxycoumarin

CAS Registry Number

939-19-5

SMILES

OC1=CC2=CC=CC=C2OC1=O

InChI Identifier

InChI=1S/C9H6O3/c10-7-5-6-3-1-2-4-8(6)12-9(7)11/h1-5,10H

InChI Key

MJKVTPMWOKAVMS-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to the coumarin skeleton.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Hydroxycoumarins

Direct Parent

Hydroxycoumarins

Alternative Parents

Substituents

Hydroxycoumarin
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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Endogenous (HMDB: HMDB0002149)

Plant

Plant (HMDB: HMDB0002149)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	369.90 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	19490 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.600 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	2.23 g/L	ALOGPS
logP	1.09	ALOGPS
logP	1.54	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	9.8	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	46.53 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	43.52 m³·mol⁻¹	ChemAxon
Polarizability	15.32 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	133.012	31661259
DarkChem	[M-H]-	130.881	31661259
DeepCCS	[M+H]+	123.407	30932474
DeepCCS	[M-H]-	119.576	30932474
DeepCCS	[M-2H]-	156.785	30932474
DeepCCS	[M+Na]+	132.228	30932474
AllCCS	[M+H]+	132.1	32859911
AllCCS	[M+H-H2O]+	127.3	32859911
AllCCS	[M+NH4]+	136.5	32859911
AllCCS	[M+Na]+	137.8	32859911
AllCCS	[M-H]-	129.3	32859911
AllCCS	[M+Na-2H]-	129.8	32859911
AllCCS	[M+HCOO]-	130.3	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	3.92 minutes	32390414
Predicted by Siyang on May 30, 2022	11.47 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.37 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1513.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	398.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	146.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	246.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	157.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	421.0 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	444.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	128.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	891.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	342.2 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	1120.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	284.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	311.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	468.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	305.5 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	109.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3 Hydroxycoumarin	OC1=CC2=CC=CC=C2OC1=O	2553.2	Standard polar	33892256
3 Hydroxycoumarin	OC1=CC2=CC=CC=C2OC1=O	1498.1	Standard non polar	33892256
3 Hydroxycoumarin	OC1=CC2=CC=CC=C2OC1=O	1528.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3 Hydroxycoumarin,1TMS,isomer #1	C[Si](C)(C)OC1=CC2=CC=CC=C2OC1=O	1821.1	Semi standard non polar	33892256
3 Hydroxycoumarin,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC2=CC=CC=C2OC1=O	2096.7	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 - 3 Hydroxycoumarin GC-MS (Non-derivatized) - 70eV, Positive	splash10-07w9-1900000000-854fe9e0cb277bdf0274	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3 Hydroxycoumarin GC-MS (1 TMS) - 70eV, Positive	splash10-00dl-4940000000-f94db70752f77b62d306	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3 Hydroxycoumarin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3 Hydroxycoumarin 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 - 3 Hydroxycoumarin 10V, Positive-QTOF	splash10-03di-0900000000-7d1955fa95d57eadbb55	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 20V, Positive-QTOF	splash10-03di-0900000000-6f0cd6d597527cbb163e	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 40V, Positive-QTOF	splash10-066r-5900000000-b0999ba2a570cafbd94b	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 10V, Negative-QTOF	splash10-03di-0900000000-bb3cef2e499cd852c2d7	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 20V, Negative-QTOF	splash10-03di-0900000000-6946524fd577f85fc413	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 40V, Negative-QTOF	splash10-0a4i-2900000000-68c22e3edc0cfd0c0975	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 10V, Negative-QTOF	splash10-03di-0900000000-c6c75fb4498190e47c4c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 20V, Negative-QTOF	splash10-03di-0900000000-5039f3724d19f475efa4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 40V, Negative-QTOF	splash10-0a4i-1900000000-41ece3466fccae6e66c6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 10V, Positive-QTOF	splash10-03di-0900000000-df7c992688619e206d43	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 20V, Positive-QTOF	splash10-03di-0900000000-39e79b46a98ff761e88f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3 Hydroxycoumarin 40V, Positive-QTOF	splash10-056r-9500000000-f07c577da7800355d236	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details

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

FDB022869

KNApSAcK ID

C00019143

Chemspider ID

13061

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6512

PubChem Compound

13650

PDB ID

Not Available

ChEBI ID

349245

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1418021

References

Synthesis Reference

Sun, Yi-feng; Song, Hua-can; Xu, Xiao-hang; Huang, Meng-wei; Xu, Zun-le. Synthesis of 3-aminocoumarin and its derivatives. Zhongshan Daxue Xuebao, Ziran Kexueban (2002), 41(6), 42-45.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

ARMSTRONG MD, SHAW KN, WALL PE: The phenolic acids of human urine; paper chromatography of phenolic acids. J Biol Chem. 1956 Jan;218(1):293-303. [PubMed:13278337 ]
Farinola N, Piller NB: CYP2A6 polymorphisms: is there a role for pharmacogenomics in preventing coumarin-induced hepatotoxicity in lymphedema patients? Pharmacogenomics. 2007 Feb;8(2):151-8. [PubMed:17286538 ]

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

3 Hydroxycoumarin → 3,4,5-trihydroxy-6-[(2-oxo-2H-chromen-3-yl)oxy]oxane-2-carboxylic acid	details

Showing metabocard for 3 Hydroxycoumarin (HMDB0002149)

MOL for HMDB0002149 (3 Hydroxycoumarin)

3D MOL for HMDB0002149 (3 Hydroxycoumarin)

3D SDF for HMDB0002149 (3 Hydroxycoumarin)

3D-SDF for HMDB0002149 (3 Hydroxycoumarin)

PDB for HMDB0002149 (3 Hydroxycoumarin)

3D PDB for HMDB0002149 (3 Hydroxycoumarin)

SMILES for HMDB0002149 (3 Hydroxycoumarin)

INCHI for HMDB0002149 (3 Hydroxycoumarin)

Structure for HMDB0002149 (3 Hydroxycoumarin)

3D Structure for HMDB0002149 (3 Hydroxycoumarin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions