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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 00:54:06 UTC

Update Date

2023-02-21 17:26:57 UTC

HMDB ID

HMDB0039437

Secondary Accession Numbers

HMDB39437

Metabolite Identification

Common Name

2,3-Dihydroxy-2,4-cyclopentadien-1-one

Description

2,3-Dihydroxy-2,4-cyclopentadien-1-one belongs to the class of organic compounds known as vinylogous acids. These are organic compounds containing a hydroxyl group, which is indirectly attached to a carbonyl via an intervening vinyl (>C=C<) moiety. 2,3-Dihydroxy-2,4-cyclopentadien-1-one has been detected, but not quantified in, several different foods, such as green tea, pulses, black tea, herbal tea, and teas (Camellia sinensis). This could make 2,3-dihydroxy-2,4-cyclopentadien-1-one a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 2,3-Dihydroxy-2,4-cyclopentadien-1-one.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₅H₄O₃

Average Molecular Weight

112.0835

Monoisotopic Molecular Weight

112.016043994

IUPAC Name

2,3-dihydroxycyclopenta-2,4-dien-1-one

Traditional Name

2,3-dihydroxycyclopenta-2,4-dien-1-one

CAS Registry Number

124902-00-7

SMILES

OC1=C(O)C(=O)C=C1

InChI Identifier

InChI=1S/C5H4O3/c6-3-1-2-4(7)5(3)8/h1-2H,(H2,6,7,8)

InChI Key

RUOZZXHSVNXNKB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as vinylogous acids. These are organic compounds containing a hydroxyl group, which is indirectly attached to a carbonyl via an intervening vinyl (>C=C<) moiety.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Vinylogous acids

Sub Class

Not Available

Direct Parent

Vinylogous acids

Alternative Parents

Substituents

Vinylogous acid
Cyclic ketone
Ketone
Enediol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Ingestion (HMDB: HMDB0039437)

Source

Exogenous

Food

Food (HMDB: HMDB0039437)

Tea

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Pulse

Pulses (FooDB: FOOD00867)

Endogenous

Plant

Plant (HMDB: HMDB0039437)
Fabaceae (HMDB: HMDB0039437)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0039437)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	208 °C	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
Water Solubility	177 g/L	ALOGPS
logP	-0.93	ALOGPS
logP	-0.15	ChemAxon
logS	0.2	ALOGPS
pKa (Strongest Acidic)	7.79	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	29.69 m³·mol⁻¹	ChemAxon
Polarizability	9.72 Å³	ChemAxon
Number of Rings	1	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
DeepCCS	[M+H]+	121.627	30932474
DeepCCS	[M-H]-	117.965	30932474
DeepCCS	[M-2H]-	155.319	30932474
DeepCCS	[M+Na]+	130.373	30932474
AllCCS	[M+H]+	125.0	32859911
AllCCS	[M+H-H2O]+	120.1	32859911
AllCCS	[M+NH4]+	129.5	32859911
AllCCS	[M+Na]+	130.8	32859911
AllCCS	[M-H]-	117.3	32859911
AllCCS	[M+Na-2H]-	119.9	32859911
AllCCS	[M+HCOO]-	122.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,3-Dihydroxy-2,4-cyclopentadien-1-one	OC1=C(O)C(=O)C=C1	2109.4	Standard polar	33892256
2,3-Dihydroxy-2,4-cyclopentadien-1-one	OC1=C(O)C(=O)C=C1	1057.1	Standard non polar	33892256
2,3-Dihydroxy-2,4-cyclopentadien-1-one	OC1=C(O)C(=O)C=C1	999.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2,3-Dihydroxy-2,4-cyclopentadien-1-one,1TMS,isomer #1	C[Si](C)(C)OC1=C(O)C(=O)C=C1	1321.4	Semi standard non polar	33892256
2,3-Dihydroxy-2,4-cyclopentadien-1-one,1TMS,isomer #2	C[Si](C)(C)OC1=C(O)C=CC1=O	1319.1	Semi standard non polar	33892256
2,3-Dihydroxy-2,4-cyclopentadien-1-one,2TMS,isomer #1	C[Si](C)(C)OC1=C(O[Si](C)(C)C)C(=O)C=C1	1445.0	Semi standard non polar	33892256
2,3-Dihydroxy-2,4-cyclopentadien-1-one,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=C(O)C(=O)C=C1	1585.6	Semi standard non polar	33892256
2,3-Dihydroxy-2,4-cyclopentadien-1-one,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=C(O)C=CC1=O	1560.4	Semi standard non polar	33892256
2,3-Dihydroxy-2,4-cyclopentadien-1-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C(=O)C=C1	1982.4	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 - 2,3-Dihydroxy-2,4-cyclopentadien-1-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-0pdi-9100000000-9ec77611ad3fd0b2009c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one GC-MS (2 TMS) - 70eV, Positive	splash10-0096-7950000000-2bd70c12325813b96b39	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 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 - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 10V, Positive-QTOF	splash10-03di-1900000000-240a8f7e991b116ed232	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 20V, Positive-QTOF	splash10-03di-4900000000-2fbadbd9647dd9e565b7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 40V, Positive-QTOF	splash10-0002-9000000000-246c53c6f568c155d7d0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 10V, Negative-QTOF	splash10-03di-0900000000-8f281824ebfbcc037ffd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 20V, Negative-QTOF	splash10-03di-0900000000-9a797c9bc000268617d5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 40V, Negative-QTOF	splash10-03di-9600000000-ef66588c06ba33f59a60	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 10V, Negative-QTOF	splash10-03di-0900000000-fb8d24398e2c2b4c8c77	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 20V, Negative-QTOF	splash10-0bt9-9400000000-2192a1d56d93e3b00851	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 40V, Negative-QTOF	splash10-0a4i-9000000000-4558b6175bb79ece3528	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 10V, Positive-QTOF	splash10-03dr-9600000000-a23cdae982887e4a49b1	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 20V, Positive-QTOF	splash10-014r-9100000000-56f2271544fd9e17cfa7	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydroxy-2,4-cyclopentadien-1-one 40V, Positive-QTOF	splash10-0ap3-9000000000-718bf1eb6b97feef77c5	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB019033

KNApSAcK ID

C00056723

Chemspider ID

15367214

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14412554

PDB ID

Not Available

ChEBI ID

173369

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

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 2,3-Dihydroxy-2,4-cyclopentadien-1-one (HMDB0039437)

MOL for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

3D MOL for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

3D SDF for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

3D-SDF for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

PDB for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

3D PDB for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

SMILES for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

INCHI for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

Structure for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

3D Structure for HMDB0039437 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra