MiMeDB: Showing metabocard for cis-Urocanate (MMDBc0000830)

Plant

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2020-12-10 23:04:45 UTC

Update Date

2025-10-07 16:04:22 UTC

Metabolite ID

MMDBc0000830

Metabolite Identification

Common Name

cis-Urocanate

Description

cis-Urocanate is a member of the imidazole derivative chemical class and is a metabolite involved in various biochemical pathways. It is primarily formed from the photochemical isomerization of trans-urocanate under UV light exposure, which is significant for its protective role in skin against UV radiation (PMID:33000155 ). In metabolic studies, cis-urocanate has been identified as a noteworthy candidate biomarker alongside other metabolites, indicating its potential relevance in metabolic profiling (PMID:38233141 ). Additionally, it is one of the major bioactive metabolites derived from histidine, alongside histamine and N-acetylhistamine, and can be quantitatively analyzed using advanced chromatographic techniques (PMID:34245620 ). Research also highlights its involvement in muscle metabolism, where it is associated with changes in metabolic pathways, including glycolytic and pentose phosphate pathways, particularly in the context of muscle fiber type adaptations (PMID:33848308 ). Furthermore, studies have shown that acupuncture can lead to significant reductions in levels of cis-urocanate among other metabolites, suggesting its dynamic role in physiological responses (PMID:39728478 ).

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 20-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUL-19         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.274   4.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.608   3.620   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      -1.608   2.080   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -2.941   4.390   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       2.393   4.390   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0      -0.274   5.930   0.000  0.00  0.00           H+0
CONECT    1    2    5   11                                                  
CONECT    2    1    6   12                                                  
CONECT    3    5    7                                                       
CONECT    4    7    8                                                       
CONECT    5    1    3    8                                                  
CONECT    6    2    9   10                                                  
CONECT    7    3    4                                                       
CONECT    8    4    5                                                       
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    1                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
(Z)-Imidazole-4-acrylic acid	ChEBI
(Z)-Imidazole-4-acrylate	Generator
(e)-Urocanate	Generator
(2E)-3-(1H-Imidazol-4-yl)acrylic acid	HMDB
(2E)-3-(1H-Imidazol-4-yl)prop-2-enoic acid	HMDB
(e)-3-(1H-Imidazol-4-yl)-2-propenoic acid	HMDB
3-(1H-Imidazol-4-yl)-(e)-2-propenoic acid	HMDB
3-(1H-Imidazol-4-yl)prop-2-enoic acid	HMDB
3-(1H-Imidazol-5-yl)-2-propenoic acid	HMDB
3-Imidazol-4-ylacrylic acid	HMDB
cis-Urocanic acid	HMDB
Imidazole-4-propene-2-enoic acid	HMDB
trans-Urocanic acid	HMDB
Urocanic acid	HMDB
Urocanic acid, cis	HMDB

Molecular Formula

C₆H₆N₂O₂

Average Mass

138.124

Monoisotopic Mass

138.042927446

IUPAC Name

(2Z)-3-(1H-imidazol-5-yl)prop-2-enoic acid

Traditional Name

(2Z)-3-(3H-imidazol-4-yl)prop-2-enoic acid

CAS Registry Number

Not Available

SMILES

[H]\C(=C(/[H])C1=CN=CN1)C(O)=O

InChI Identifier

InChI=1S/C6H6N2O2/c9-6(10)2-1-5-3-7-4-8-5/h1-4H,(H,7,8)(H,9,10)/b2-1-

InChI Key

LOIYMIARKYCTBW-UPHRSURJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as imidazolyl carboxylic acids and derivatives. These are organic compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azoles

Sub Class

Imidazoles

Direct Parent

Imidazolyl carboxylic acids and derivatives

Alternative Parents

Substituents

Imidazolyl carboxylic acid derivative
Heteroaromatic compound
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

urocanic acid (CHEBI:30818 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	21 g/L	ALOGPS
logP	0	ALOGPS
logP	-0.88	ChemAxon
logS	-0.82	ALOGPS
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	6.82	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	65.98 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	35.89 m³·mol⁻¹	ChemAxon
Polarizability	12.75 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9500000000-214759fcc6a8a9e5c0fe	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9500000000-79bb3529b72209d3d144	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0079-1900000000-dac4165382f541a26a03	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0076-8900000000-6da8eb6b76055856b714	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-014i-9000000000-ab76de8a8f1873f63de6	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-1900000000-173e1f32b118424e132d	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000l-5900000000-b1ebc285fc95a34dc7b1	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9200000000-66f717c0018108bc7769	2016-08-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	264.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	149.8
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	40.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	239.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	266.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	315.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	564.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	573.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	646.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	189.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	325.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	204.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	61.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	191.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	583.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	58.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	256.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	745.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	576.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	cis-Urocanate_TMS_1	C[Si](C)(C)OC(=O)/C=C\C1=CN=C[NH]1	standard non polar	2025-10-23	2127.34
Gas Chromatography	cis-Urocanate_TMS_2	C[Si](C)(C)N1C=NC=C1/C=C\C(=O)O	standard non polar	2025-10-23	1718.88
Gas Chromatography	cis-Urocanate_TMS_3	C[Si](C)(C)OC(=O)/C=C\C1=CN=CN1[Si](C)(C)C	standard non polar	2025-10-23	2376.35
Gas Chromatography	cis-Urocanate_TMS_1	C[Si](C)(C)OC(=O)/C=C\C1=CN=C[NH]1	standard polar	2025-10-23	2138.38
Gas Chromatography	cis-Urocanate_TMS_2	C[Si](C)(C)N1C=NC=C1/C=C\C(=O)O	standard polar	2025-10-23	2295.18
Gas Chromatography	cis-Urocanate_TMS_3	C[Si](C)(C)OC(=O)/C=C\C1=CN=CN1[Si](C)(C)C	standard polar	2025-10-23	2012.56

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Verrucomicrobia	1	Human feces; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Firmicutes	3	Human ; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque; Human feces; Human sputum; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0034174

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB012465

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

1549103

PDB ID

Not Available

ChEBI ID

30818

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Showing metabocard for cis-Urocanate (MMDBc0000830)

MOL for #<Metabolite:0x00007f9adb3ff458>

3D MOL for #<Metabolite:0x00007f9adb3ff458>

3D SDF for #<Metabolite:0x00007f9adb3ff458>

3D-SDF for #<Metabolite:0x00007f9adb3ff458>

PDB for #<Metabolite:0x00007f9adb3ff458>

3D PDB for #<Metabolite:0x00007f9adb3ff458>

SMILES for #<Metabolite:0x00007f9adb3ff458>

INCHI for #<Metabolite:0x00007f9adb3ff458>

Structure for #<Metabolite:0x00007f9adb3ff458>

3D Structure for #<Metabolite:0x00007f9adb3ff458>