MiMeDB: Showing metabocard for Syringic acid (MMDBc0000405)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:37:01 UTC

Update Date

2024-10-06 20:02:44 UTC

Metabolite ID

MMDBc0000405

Metabolite Identification

Common Name

Syringic acid

Description

Syringic acid, also known as syringate or cedar acid, belongs to the class of organic compounds known as gallic acid and derivatives. Gallic acid and derivatives are compounds containing a 3,4,5-trihydroxybenzoic acid moiety. Outside of the human body, Syringic acid is found, on average, in the highest concentration within a few different foods, such as common walnuts, swiss chards, and olives and in a lower concentration in apples, tarragons, and peanuts. Syringic acid has also been detected, but not quantified in several different foods, such as sweet marjorams, silver lindens, bulgurs, annual wild rices, and barley. This could make syringic acid a potential biomarker for the consumption of these foods. Syringic acid is correlated with high antioxidant activity and inhibition of LDL oxidation. Research suggests that phenolics from wine may play a positive role against oxidation of low-density lipoprotein (LDL), which is a key step in the development of atherosclerosis. Syringic acid is a phenol present in some distilled alcohol beverages. It is also a product of microbial (gut) metabolism of anthocyanins and other polyphenols that have been consumed (in fruits and alcoholic beverages - PMID:18767860 ). Syringic acid is also a microbial metabolite that can be found in Bifidobacterium (PMID:24958563 ).

Structure

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

Syringic acid
  Mrv1652305201900042D          

 14 14  0  0  0  0            999 V2000
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  2  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000405

> <DATABASE_NAME>
MIME

> <SMILES>
COC1=CC(=CC(OC)=C1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H10O5/c1-13-6-3-5(9(11)12)4-7(14-2)8(6)10/h3-4,10H,1-2H3,(H,11,12)

> <INCHI_KEY>
JMSVCTWVEWCHDZ-UHFFFAOYSA-N

> <FORMULA>
C9H10O5

> <MOLECULAR_WEIGHT>
198.174

> <EXACT_MASS>
198.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
18.770948525158104

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-hydroxy-3,5-dimethoxybenzoic acid

> <ALOGPS_LOGP>
1.55

> <JCHEM_LOGP>
1.0119208709999998

> <ALOGPS_LOGS>
-1.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.550188846644089

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.931934806367758

> <JCHEM_PKA_STRONGEST_BASIC>
-4.61219102745602

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
48.221500000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.71e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
syringic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Syringic acid                                     
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAY-19         0                                  
HETATM    1  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    7    3   11                                                  
CONECT   11   10                                                            
CONECT   12    5   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
Cedar acid	ChEBI
Gallic acid 3,5-dimethyl ether	ChEBI
Syringate	Kegg
4-Hydroxy-3,5-dimethoxybenzoate	Kegg
Gallate 3,5-dimethyl ether	Generator
4-Hydroxy-3,5-dimethoxybenzoic acid	Generator
Syringic acid cu (+2) salt (1:1)	MeSH
3,5-Dimethoxy-4-hydroxybenzoate	HMDB
3,5-Dimethoxy-4-hydroxybenzoic acid	HMDB
3,5-Dimethoxybenzoyl hydrazine	HMDB
3,5-Dimethyl-4-hydroxybenzoate	HMDB
3,5-Dimethyl-4-hydroxybenzoic acid	HMDB
4-Hydroxy-3,5-dimethylbenzoate	HMDB
4-Hydroxy-3,5-dimethylbenzoic acid	HMDB
Syringlicacid	HMDB
Syringic acid	HMDB
3,5-dimethoxygallic acid	HMDB
3,5-O-dimethylgallic acid	HMDB

Molecular Formula

C₉H₁₀O₅

Average Mass

198.174

Monoisotopic Mass

198.052823422

IUPAC Name

4-hydroxy-3,5-dimethoxybenzoic acid

Traditional Name

syringic acid

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1O)C(O)=O

InChI Identifier

InChI=1S/C9H10O5/c1-13-6-3-5(9(11)12)4-7(14-2)8(6)10/h3-4,10H,1-2H3,(H,11,12)

InChI Key

JMSVCTWVEWCHDZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gallic acid and derivatives. Gallic acid and derivatives are compounds containing a 3,4,5-trihydroxybenzoic acid moiety.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Gallic acid and derivatives

Alternative Parents

Substituents

Gallic acid or derivatives
M-methoxybenzoic acid or derivatives
M-dimethoxybenzene
Dimethoxybenzene
Methoxyphenol
Benzoic acid
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Benzoyl
Alkyl aryl ether
Phenol
Carboxylic acid derivative
Carboxylic acid
Ether
Monocarboxylic acid or derivatives
Organooxygen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

phenols (CHEBI:68329 )
dimethoxybenzene (CHEBI:68329 )
benzoic acids (CHEBI:68329 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.71 g/L	ALOGPS
logP	1.55	ALOGPS
logP	1.01	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	3.93	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	48.22 m³·mol⁻¹	ChemAxon
Polarizability	18.77 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Saliva
Urine

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192140	UDP-glucuronosyltransferase 1-1	Enzyme	P22309	Homo sapiens
MMDBp0194143	Glycine N-acyltransferase	Enzyme	Q6IB77	Homo sapiens
MMDBp0197061	Sulfotransferase 1A3	Enzyme	P0DMM9	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Free radical scavenger		Chemical reaction		Pubchem	28415050

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference
General Exposome	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Urine	Detected but not Quantified						NULL	NULL	Consuming polyphenols described by Phenol-Explorer entry 420	HMDB	12771321
Human Blood	Detected and Quantified			0	7.1	uM	Adult (>18 years old)	Male	Normal	HMDB	16019270
Human Urine	Detected and Quantified	0.9	0.2			umol/mmol creatinine	Adult (>18 years old)	Not Specified	Normal	HMDB	16939358
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Hypertension (mild)	HMDB	20013882
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Hypertension (mild)	HMDB	20013882
Human Feces	Detected and Quantified	2.119				nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	24010549
Human Feces	Detected and Quantified	9.285	5.601			nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	24010549
Human Feces	Detected and Quantified	3.885	1.867			nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	24010549
Human Urine	Detected and Quantified	1.5				umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Colorectal cancer	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected and Quantified	2.155		0.121	6.0704	nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	28029051
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Saliva	Detected and Quantified	1.59	0.118			uM	Adult (>18 years old)	Not Specified	Normal	HMDB	Sugimoto, M., Saruta, J., Matsuki, C. et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles. Metabolomics, 9, 454–463 (2013). https://doi.org/10.1007/s11306-012-0464-y
Human Saliva	Detected and Quantified	1.57	0.123			uM	Adult (>18 years old)	Both	Normal	HMDB	Sugimoto, M., Saruta, J., Matsuki, C. et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles. Metabolomics, 9, 454–463 (2013). https://doi.org/10.1007/s11306-012-0464-y
Human Saliva	Detected and Quantified	1.62	0.105			uM	Adult (>18 years old)	Both	Normal	HMDB	Sugimoto, M., Saruta, J., Matsuki, C. et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles. Metabolomics, 9, 454–463 (2013). https://doi.org/10.1007/s11306-012-0464-y
Human Saliva	Detected and Quantified	1.71	0.0913			uM	Adult (>18 years old)	Male	Normal	HMDB	Sugimoto, M., Saruta, J., Matsuki, C. et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles. Metabolomics, 9, 454–463 (2013). https://doi.org/10.1007/s11306-012-0464-y
Human Urine	Detected and Quantified	1.5				umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Feces	Detected and Quantified	2.119				nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	24010549
Human Blood	Detected and Quantified			0.0	7.1	uM	Adult (>18 years old)	Male	Normal	HMDB	16019270
Human Urine	Detected and Quantified	0.9	0.2			umol/mmol creatinine	Adult (>18 years old)	Not Specified	Normal	HMDB	16939358
Human Feces	Detected and Quantified	2.155		0.121	6.0704	nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	28029051
Human Feces	Detected and Quantified	3.885	1.867			nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	24010549
Human Feces	Detected and Quantified	9.285	5.601			nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	24010549
Human Saliva	Detected and Quantified	1.57	0.123			uM	Adult (>18 years old)	Both	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	1.59	0.118			uM	Adult (>18 years old)	Not Specified	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	1.62	0.105			uM	Adult (>18 years old)	Both	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	1.71	0.0913			uM	Adult (>18 years old)	Male	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0002085

DrugBank ID

Not Available

Phenol Explorer Compound ID

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Syringic_acid

METLIN ID

2256

PubChem Compound

10742

PDB ID

Not Available

ChEBI ID

68329

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Kalkan Yildirim H, Delen Akcay Y, Guvenc U, Yildirim Sozmen E: Protection capacity against low-density lipoprotein oxidation and antioxidant potential of some organic and non-organic wines. Int J Food Sci Nutr. 2004 Aug;55(5):351-62. doi: 10.1080/09637480412331319781. [PubMed:15545043 ]
Forester SC, Waterhouse AL: Identification of Cabernet Sauvignon anthocyanin gut microflora metabolites. J Agric Food Chem. 2008 Oct 8;56(19):9299-304. doi: 10.1021/jf801309n. Epub 2008 Sep 4. [PubMed:18767860 ]
Boto-Ordonez M, Urpi-Sarda M, Queipo-Ortuno MI, Tulipani S, Tinahones FJ, Andres-Lacueva C: High levels of Bifidobacteria are associated with increased levels of anthocyanin microbial metabolites: a randomized clinical trial. Food Funct. 2014 Aug;5(8):1932-8. doi: 10.1039/c4fo00029c. [PubMed:24958563 ]

Showing metabocard for Syringic acid (MMDBc0000405)

MOL for #<Metabolite:0x00007f922171b690>

3D MOL for #<Metabolite:0x00007f922171b690>

3D SDF for #<Metabolite:0x00007f922171b690>

3D-SDF for #<Metabolite:0x00007f922171b690>

PDB for #<Metabolite:0x00007f922171b690>

3D PDB for #<Metabolite:0x00007f922171b690>

SMILES for #<Metabolite:0x00007f922171b690>

INCHI for #<Metabolite:0x00007f922171b690>

Structure for #<Metabolite:0x00007f922171b690>

3D Structure for #<Metabolite:0x00007f922171b690>