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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 16:40:47 UTC

Update Date

2021-09-23 16:40:48 UTC

HMDB ID

HMDB0302296

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Arctic acid C

Description

Arctic acid c, also known as arctate c, is a member of the class of compounds known as bi- and oligothiophenes. Bi- and oligothiophenes are organic compounds containing two or more linked thiophene rings. Thiophene is a five-member aromatic ring with one sulfur and four carbon atoms. Arctic acid c is practically insoluble (in water) and a weakly acidic compound (based on its pKa). Arctic acid c can be found in burdock, which makes arctic acid c a potential biomarker for the consumption of this food product.

Structure

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


  Mrv0541 02241223312D          

 18 19  0  0  0  0            999 V2000
   -3.3839    1.9806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7237    1.4858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8060    0.6597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1459    0.1648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1459   -0.6597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3206   -0.9071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8249   -0.2470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3206    0.4123    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.8977   -1.9806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9806   -1.1554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.6597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.1648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4944    0.4123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0004   -0.2470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4944   -0.9071    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8060   -0.0004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7230   -0.8249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3839   -1.3198    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  3  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  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
  7 14  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 17  1  0  0  0  0
 11 12  2  0  0  0  0
 11 15  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302296

> <DATABASE_NAME>
hmdb

> <SMILES>
CC#CC1=CC=C(S1)C1=CC=C(S1)C(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H10O3S2/c1-2-3-8-4-5-9(17-8)10-6-7-11(18-10)12(14)13(15)16/h4-7,12,14H,1H3,(H,15,16)

> <INCHI_KEY>
YUIKESNQNJLOMW-UHFFFAOYSA-N

> <FORMULA>
C13H10O3S2

> <MOLECULAR_WEIGHT>
278.347

> <EXACT_MASS>
278.007135566

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
28.899101701880145

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-hydroxy-2-{5-[5-(prop-1-yn-1-yl)thiophen-2-yl]thiophen-2-yl}acetic acid

> <ALOGPS_LOGP>
3.06

> <JCHEM_LOGP>
3.34950131

> <ALOGPS_LOGS>
-4.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.080439637168706

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.639473404769638

> <JCHEM_PKA_STRONGEST_BASIC>
-4.3248063464091695

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
67.86110000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.94e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hydroxy({5-[5-(prop-1-yn-1-yl)thiophen-2-yl]thiophen-2-yl})acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -6.317   3.697   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.084   2.773   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.238   1.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.006   0.308   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.006  -1.231   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.465  -1.693   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.540  -0.461   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0      -2.465   0.770   0.000  0.00  0.00           S+0
HETATM    9  O   UNK     0       3.542  -3.697   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.697  -2.157   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.310  -1.231   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.310   0.308   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.923   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.001  -0.461   0.000  0.00  0.00           C+0
HETATM   15  S   UNK     0       0.923  -1.693   0.000  0.00  0.00           S+0
HETATM   16  O   UNK     0       5.238  -0.001   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.083  -1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.317  -2.464   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   14                                                  
CONECT    8    4    7                                                       
CONECT    9   10                                                            
CONECT   10    9   11   17                                                  
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14    7   13   15                                                  
CONECT   15   11   14                                                       
CONECT   16   17                                                            
CONECT   17   10   16   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0302296
HETATM    1  C1  UNL     1       7.339   0.175   0.568  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.920   0.145   0.208  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.750   0.100  -0.090  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.335   0.049  -0.425  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.765  -0.214  -1.639  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.430  -0.208  -1.716  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.740   0.062  -0.565  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.720   0.132  -0.361  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.725  -0.051  -1.255  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.990   0.075  -0.790  1.00  0.00           C  
HETATM   11  C11 UNL     1      -3.143   0.374   0.532  1.00  0.00           C  
HETATM   12  C12 UNL     1      -4.416   0.574   1.317  1.00  0.00           C  
HETATM   13  O1  UNL     1      -4.263  -0.158   2.498  1.00  0.00           O  
HETATM   14  C13 UNL     1      -5.529  -0.015   0.564  1.00  0.00           C  
HETATM   15  O2  UNL     1      -5.897   0.530  -0.503  1.00  0.00           O  
HETATM   16  O3  UNL     1      -6.188  -1.160   0.996  1.00  0.00           O  
HETATM   17  S1  UNL     1      -1.522   0.472   1.092  1.00  0.00           S  
HETATM   18  S2  UNL     1       1.979   0.298   0.581  1.00  0.00           S  
HETATM   19  H1  UNL     1       7.917   0.910   0.008  1.00  0.00           H  
HETATM   20  H2  UNL     1       7.709  -0.876   0.413  1.00  0.00           H  
HETATM   21  H3  UNL     1       7.488   0.376   1.651  1.00  0.00           H  
HETATM   22  H4  UNL     1       3.417  -0.420  -2.509  1.00  0.00           H  
HETATM   23  H5  UNL     1       0.847  -0.407  -2.646  1.00  0.00           H  
HETATM   24  H6  UNL     1      -1.531  -0.295  -2.331  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.897  -0.055  -1.433  1.00  0.00           H  
HETATM   26  H8  UNL     1      -4.572   1.665   1.525  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.634   0.366   3.081  1.00  0.00           H  
HETATM   28  H10 UNL     1      -5.610  -1.955   1.228  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    3    3
CONECT    3    4
CONECT    4    5    5   18
CONECT    5    6   22
CONECT    6    7    7   23
CONECT    7    8   18
CONECT    8    9    9   17
CONECT    9   10   24
CONECT   10   11   11   25
CONECT   11   12   17
CONECT   12   13   14   26
CONECT   13   27
CONECT   14   15   15   16
CONECT   16   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Hydroxy-2-[5'-(prop-1-yn-1-yl)-[2,2'-bithiophene]-5-yl]acetate	Generator
Arctate C	Generator

Chemical Formula

C₁₃H₁₀O₃S₂

Average Molecular Weight

278.347

Monoisotopic Molecular Weight

278.007135566

IUPAC Name

2-hydroxy-2-{5-[5-(prop-1-yn-1-yl)thiophen-2-yl]thiophen-2-yl}acetic acid

Traditional Name

hydroxy({5-[5-(prop-1-yn-1-yl)thiophen-2-yl]thiophen-2-yl})acetic acid

CAS Registry Number

Not Available

SMILES

CC#CC1=CC=C(S1)C1=CC=C(S1)C(O)C(O)=O

InChI Identifier

InChI=1S/C13H10O3S2/c1-2-3-8-4-5-9(17-8)10-6-7-11(18-10)12(14)13(15)16/h4-7,12,14H,1H3,(H,15,16)

InChI Key

YUIKESNQNJLOMW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bi- and oligothiophenes. These are organic compounds containing two or more linked thiophene rings. Thiophene is a five-member aromatic ring with one sulfur and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Bi- and oligothiophenes

Sub Class

Not Available

Direct Parent

Bi- and oligothiophenes

Alternative Parents

Substituents

Bithiophene
2,5-disubstituted thiophene
Alpha-hydroxy acid
Hydroxy acid
Heteroaromatic compound
Thiophene
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Alcohol
Organooxygen compound
Aromatic alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Exogenous (HMDB: HMDB0302296)

Food

Vegetable

Root vegetable

Burdock (FooDB: FOOD00017)

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	3.06	ALOGPS
logP	3.35	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	3.64	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	67.86 m³·mol⁻¹	ChemAxon
Polarizability	28.9 Å³	ChemAxon
Number of Rings	2	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
AllCCS	[M+H]+	160.659	32859911
AllCCS	[M+H-H2O]+	156.926	32859911
AllCCS	[M+Na]+	165.124	32859911
AllCCS	[M+NH4]+	164.126	32859911
AllCCS	[M-H]-	159.057	32859911
AllCCS	[M+Na-2H]-	158.83	32859911
AllCCS	[M+HCOO]-	158.709	32859911
DeepCCS	[M+H]+	154.164	30932474
DeepCCS	[M-H]-	151.806	30932474
DeepCCS	[M-2H]-	184.81	30932474
DeepCCS	[M+Na]+	160.258	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	12.6754 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.92 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1894.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	392.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	142.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	227.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	202.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	457.9 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	525.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	87.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1029.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	430.1 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	1207.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	352.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	347.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	338.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	249.6 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	36.7 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 10V, Positive-QTOF	splash10-01t9-0090000000-4b5b7e30f9c9289b0705	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 20V, Positive-QTOF	splash10-0m93-2790000000-a2dc6cb08cab45f8b9ec	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 40V, Positive-QTOF	splash10-0udi-9540000000-8b7302c34bbfa0cc59bb	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 10V, Negative-QTOF	splash10-004i-1290000000-5eb975e48c6b89c03a95	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 20V, Negative-QTOF	splash10-053r-1980000000-43f79659905089e23076	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 40V, Negative-QTOF	splash10-0089-9800000000-dde059ce5ed0bdeb1bf7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 10V, Positive-QTOF	splash10-004i-0090000000-3d40d3050b02ab8c05d6	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 20V, Positive-QTOF	splash10-03fr-0090000000-13bcf4fd6857f156e579	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 40V, Positive-QTOF	splash10-0ufr-3950000000-8d8e5cc54d3b55e2e565	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 10V, Negative-QTOF	splash10-004i-0090000000-f02b159df33777b05513	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 20V, Negative-QTOF	splash10-0f6x-0390000000-20722fdacf635fb58aa7	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arctic acid C 40V, Negative-QTOF	splash10-000t-2900000000-2013bcee9c212f1af7d4	2021-10-21	Wishart 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

FDB004072

KNApSAcK ID

Not Available

Chemspider ID

32699475

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71587384

PDB ID

Not Available

ChEBI ID

Not Available

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

Not Available

Showing metabocard for Arctic acid C (HMDB0302296)

MOL for HMDB0302296 (Arctic acid C)

3D MOL for HMDB0302296 (Arctic acid C)

3D SDF for HMDB0302296 (Arctic acid C)

3D-SDF for HMDB0302296 (Arctic acid C)

PDB for HMDB0302296 (Arctic acid C)

3D PDB for HMDB0302296 (Arctic acid C)

SMILES for HMDB0302296 (Arctic acid C)

INCHI for HMDB0302296 (Arctic acid C)

Structure for HMDB0302296 (Arctic acid C)

3D Structure for HMDB0302296 (Arctic acid C)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra