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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 20:05:24 UTC

Update Date

2022-03-07 02:54:23 UTC

HMDB ID

HMDB0035145

Secondary Accession Numbers

HMDB35145

Metabolite Identification

Common Name

Chrycolide

Description

Chrycolide belongs to the class of organic compounds known as benzofuranones. These are organic compounds containing a benzene ring fused to a furanone. Chrycolide has been detected, but not quantified in, herbs and spices. This could make chrycolide a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Chrycolide.

Structure

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


  Mrv0541 05061308152D          

 16 18  0  0  0  0            999 V2000
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403    2.9445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403    2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249    3.1994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249    1.8646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0098    2.5320    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  2  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  5  2  0  0  0  0
 10  7  2  0  0  0  0
 10  8  1  0  0  0  0
 11  7  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  8  1  0  0  0  0
 14 12  2  0  0  0  0
 15 11  1  0  0  0  0
 15 12  1  0  0  0  0
 16  6  1  0  0  0  0
 16  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035145

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC=CC2=C1C(=O)OC2C1=CC=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C12H8O3S/c13-8-4-1-3-7-10(8)12(14)15-11(7)9-5-2-6-16-9/h1-6,11,13H

> <INCHI_KEY>
CLGIBOHWUJNNKL-UHFFFAOYSA-N

> <FORMULA>
C12H8O3S

> <MOLECULAR_WEIGHT>
232.255

> <EXACT_MASS>
232.019414812

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
22.35337090683048

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-hydroxy-3-(thiophen-2-yl)-1,3-dihydro-2-benzofuran-1-one

> <ALOGPS_LOGP>
3.25

> <JCHEM_LOGP>
3.5715063199999997

> <ALOGPS_LOGS>
-2.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.286239159376557

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.550317975253492

> <JCHEM_PKA_STRONGEST_BASIC>
-4.303145964268659

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
59.791500000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.38e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-hydroxy-3-(thiophen-2-yl)-3H-2-benzofuran-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.382   5.496   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.382   3.956   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.846   5.972   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.846  -1.941   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.417   0.770   0.000  0.00  0.00           O+0
HETATM   16  S   UNK     0       3.752   4.726   0.000  0.00  0.00           S+0
CONECT    1    3    4                                                       
CONECT    2    5    6                                                       
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9                                                       
CONECT    6    2   16                                                       
CONECT    7    3   10   11                                                  
CONECT    8    4   10   13                                                  
CONECT    9    5   11   16                                                  
CONECT   10    7    8   12                                                  
CONECT   11    7    9   15                                                  
CONECT   12   10   14   15                                                  
CONECT   13    8                                                            
CONECT   14   12                                                            
CONECT   15   11   12                                                       
CONECT   16    6    9                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
7-Hydroxy-3-(2-thienyl)-1(3H)-isobenzofuranone, 9ci	HMDB

Chemical Formula

C₁₂H₈O₃S

Average Molecular Weight

232.255

Monoisotopic Molecular Weight

232.019414812

IUPAC Name

7-hydroxy-3-(thiophen-2-yl)-1,3-dihydro-2-benzofuran-1-one

Traditional Name

7-hydroxy-3-(thiophen-2-yl)-3H-2-benzofuran-1-one

CAS Registry Number

91362-91-3

SMILES

OC1=CC=CC2=C1C(=O)OC2C1=CC=CS1

InChI Identifier

InChI=1S/C12H8O3S/c13-8-4-1-3-7-10(8)12(14)15-11(7)9-5-2-6-16-9/h1-6,11,13H

InChI Key

CLGIBOHWUJNNKL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzofuranones. These are organic compounds containing a benzene ring fused to a furanone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzofurans

Sub Class

Benzofuranones

Direct Parent

Benzofuranones

Alternative Parents

Substituents

Benzofuranone
Phthalide
Isobenzofuranone
Isocoumaran
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Thiophene
Vinylogous acid
Heteroaromatic compound
Lactone
Carboxylic acid ester
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0035145)
Cell membrane (HMDB: HMDB0035145)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0035145)

Source

Exogenous

Exogenous (HMDB: HMDB0035145)

Food

Food (HMDB: HMDB0035145)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Plant

Plant (HMDB: HMDB0035145)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0035145)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	115 - 116 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	344.2 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.24 g/L	ALOGPS
logP	3.25	ALOGPS
logP	3.57	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.55	ChemAxon
pKa (Strongest Basic)	-4.3	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	1	ChemAxon
Refractivity	59.79 m³·mol⁻¹	ChemAxon
Polarizability	22.35 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	150.077	31661259
DarkChem	[M-H]-	148.106	31661259
DeepCCS	[M+H]+	144.499	30932474
DeepCCS	[M-H]-	142.103	30932474
DeepCCS	[M-2H]-	176.503	30932474
DeepCCS	[M+Na]+	150.823	30932474
AllCCS	[M+H]+	149.3	32859911
AllCCS	[M+H-H2O]+	145.2	32859911
AllCCS	[M+NH4]+	153.2	32859911
AllCCS	[M+Na]+	154.4	32859911
AllCCS	[M-H]-	149.2	32859911
AllCCS	[M+Na-2H]-	148.7	32859911
AllCCS	[M+HCOO]-	148.2	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.	6.37 minutes	32390414
Predicted by Siyang on May 30, 2022	18.0027 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.01 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2466.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	613.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	250.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	436.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	458.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	759.4 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	825.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	352.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1567.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	575.4 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	1562.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	565.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	526.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	619.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	432.4 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	75.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Chrycolide	OC1=CC=CC2=C1C(=O)OC2C1=CC=CS1	3256.4	Standard polar	33892256
Chrycolide	OC1=CC=CC2=C1C(=O)OC2C1=CC=CS1	2001.3	Standard non polar	33892256
Chrycolide	OC1=CC=CC2=C1C(=O)OC2C1=CC=CS1	2043.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Chrycolide,1TMS,isomer #1	C[Si](C)(C)OC1=CC=CC2=C1C(=O)OC2C1=CC=CS1	2131.8	Semi standard non polar	33892256
Chrycolide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=CC2=C1C(=O)OC2C1=CC=CS1	2383.3	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 - Chrycolide GC-MS (Non-derivatized) - 70eV, Positive	splash10-0ha0-5980000000-2cbf4753c14d7b2a6dd3	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Chrycolide GC-MS (1 TMS) - 70eV, Positive	splash10-022i-7690000000-c746335e32c45288f292	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Chrycolide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Chrycolide 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 - Chrycolide 10V, Positive-QTOF	splash10-001i-0090000000-b5c2ad04d0b036b7a6eb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 20V, Positive-QTOF	splash10-001i-0190000000-f33850ac6505bf933e38	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 40V, Positive-QTOF	splash10-0fkc-4910000000-27f9bc378f3c03ed4382	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 10V, Negative-QTOF	splash10-001i-0090000000-7383fb280eab0e191575	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 20V, Negative-QTOF	splash10-001i-0390000000-a14d3c2ffb1104626031	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 40V, Negative-QTOF	splash10-0a4i-9200000000-928127cd9a4fcfb398fa	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 10V, Negative-QTOF	splash10-001i-0090000000-92b32ffbce63ff7ed741	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 20V, Negative-QTOF	splash10-001i-0090000000-6bf2e7e8e3474e82e17c	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 40V, Negative-QTOF	splash10-03k9-0910000000-6f47f458d9ff41c7a12b	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 10V, Positive-QTOF	splash10-001i-0090000000-e81bb5555e2eaac4fab1	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 20V, Positive-QTOF	splash10-001i-0090000000-e81bb5555e2eaac4fab1	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Chrycolide 40V, Positive-QTOF	splash10-0iki-1930000000-ee20cde1dc88bc67e33e	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

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

FDB013781

KNApSAcK ID

C00055326

Chemspider ID

26774554

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13259263

PDB ID

Not Available

ChEBI ID

169131

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1847961

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 Chrycolide (HMDB0035145)

MOL for HMDB0035145 (Chrycolide)

3D MOL for HMDB0035145 (Chrycolide)

3D SDF for HMDB0035145 (Chrycolide)

3D-SDF for HMDB0035145 (Chrycolide)

PDB for HMDB0035145 (Chrycolide)

3D PDB for HMDB0035145 (Chrycolide)

SMILES for HMDB0035145 (Chrycolide)

INCHI for HMDB0035145 (Chrycolide)

Structure for HMDB0035145 (Chrycolide)

3D Structure for HMDB0035145 (Chrycolide)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra