MiMeDB: Showing metabocard for hercynine (MMDBc0056024)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:13:37 UTC

Update Date

2025-10-07 16:04:20 UTC

Metabolite ID

MMDBc0056024

Metabolite Identification

Common Name

hercynine

Description

Hercynine is a betaine metabolite classified within the chemical class of amino acid derivatives. Its chemical structure features an imidazole ring, which is pivotal in its biochemical functions. Hercynine is involved in several metabolic pathways, notably in the degradation of glutamine and histidine. It is produced from ergothioneine sulfinate through the action of an aminohydrolase, releasing sulfite in the process (PMID:40480087 ). Subsequently, hercynine can be converted into urocanate, a key metabolite in histidine catabolism, by an aromatic amino acid lyase (PMID:40480087 ). Additionally, hercynine levels are associated with various conditions, such as prostatitis, where they reflect genetic susceptibility linked to metabolic phenotypes (PMID:40697619 ). Furthermore, its abundance in the stroma compared to other tissue sections highlights its potential role in physiological processes (PMID:39934578 ). The interplay between hercynine and immune cell activity is also noted, particularly in conditions like PCOS, where it mediates associations with alpha-ketoglutarate and ornithine ratios (PMID:40123755 ). Overall, hercynine's involvement in these metabolic pathways underscores its significance in both health and disease contexts.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222132D          

 15 15  0  0  1  0            999 V2000
    1.2822    4.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4572    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1072    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9967    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.7112    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    1.1143    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2822    1.5268    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  4  1  6  0  0  0
  9  8  1  0  0  0  0
 10  5  1  0  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  1  1  0  0  0  0
 12  2  1  0  0  0  0
 12  3  1  0  0  0  0
 12  8  1  0  0  0  0
 13  9  2  0  0  0  0
 14  9  1  0  0  0  0
  8 15  1  1  0  0  0
M  CHG  2  12   1  14  -1
M  END
> <DATABASE_ID>
MMDBc0056024

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](CC1=CN=CN1)(C([O-])=O)[N+](C)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C9H15N3O2/c1-12(2,3)8(9(13)14)4-7-5-10-6-11-7/h5-6,8H,4H2,1-3H3,(H-,10,11,13,14)/t8-/m0/s1

> <INCHI_KEY>
GPPYTCRVKHULJH-QMMMGPOBSA-N

> <FORMULA>
C9H15N3O2

> <MOLECULAR_WEIGHT>
197.238

> <EXACT_MASS>
197.116426735

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
20.180534196874355

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-3-(1H-imidazol-5-yl)-2-(trimethylazaniumyl)propanoate

> <JCHEM_LOGP>
-4.51732507242313

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.822982942245382

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.025270364061525

> <JCHEM_PKA_STRONGEST_BASIC>
6.7044239385636715

> <JCHEM_POLAR_SURFACE_AREA>
68.81

> <JCHEM_REFRACTIVITY>
74.879

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-(3H-imidazol-4-yl)-2-(trimethylammonio)propanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       2.393   7.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.853   5.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.933   5.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.393   4.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.727   3.620   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       2.393   5.930   0.000  0.00  0.00           N+1
HETATM   13  O   UNK     0       5.061   4.390   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       3.727   2.080   0.000  0.00  0.00           O-1
HETATM   15  H   UNK     0       2.393   2.850   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2   12                                                            
CONECT    3   12                                                            
CONECT    4    7    8                                                       
CONECT    5    7   10                                                       
CONECT    6   10   11                                                       
CONECT    7    4    5   11                                                  
CONECT    8    4    9   12   15                                             
CONECT    9    8   13   14                                                  
CONECT   10    5    6                                                       
CONECT   11    6    7                                                       
CONECT   12    1    2    3    8                                             
CONECT   13    9                                                            
CONECT   14    9                                                            
CONECT   15    8                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

Synonyms

Value	Source
(S)-alpha-Carboxy-N,N,N-trimethyl-1H-imidazole-4-ethanaminium hydroxide, inner salt	ChEBI
Nalpha,nalpha,nalpha-trimethyl-L-histidine	ChEBI
(S)-a-Carboxy-N,N,N-trimethyl-1H-imidazole-4-ethanaminium hydroxide, inner salt	Generator
(S)-Α-carboxy-N,N,N-trimethyl-1H-imidazole-4-ethanaminium hydroxide, inner salt	Generator

Molecular Formula

C₉H₁₅N₃O₂

Average Mass

197.238

Monoisotopic Mass

197.116426735

IUPAC Name

(2S)-3-(1H-imidazol-5-yl)-2-(trimethylazaniumyl)propanoate

Traditional Name

(2S)-3-(3H-imidazol-4-yl)-2-(trimethylammonio)propanoate

CAS Registry Number

Not Available

SMILES

[H][C@](CC1=CN=CN1)(C([O-])=O)[N+](C)(C)C

InChI Identifier

InChI=1S/C9H15N3O2/c1-12(2,3)8(9(13)14)4-7-5-10-6-11-7/h5-6,8H,4H2,1-3H3,(H-,10,11,13,14)/t8-/m0/s1

InChI Key

GPPYTCRVKHULJH-QMMMGPOBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Histidine and derivatives

Alternative Parents

Substituents

Histidine or derivatives
Alpha-amino acid
L-alpha-amino acid
Imidazolyl carboxylic acid derivative
Aralkylamine
Azole
Imidazole
Tetraalkylammonium salt
Heteroaromatic compound
Quaternary ammonium salt
Carboxylic acid salt
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Amine
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organopnictogen compound
Carbonyl group
Organic zwitterion
Organic salt
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

N(alpha)-methyl-L-histidines (CHEBI:15781 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.5	ChemAxon
pKa (Strongest Acidic)	2.03	ChemAxon
pKa (Strongest Basic)	6.7	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	68.81 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	74.88 m³·mol⁻¹	ChemAxon
Polarizability	20.18 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

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

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
Bacteria/Eubacteria	Actinobacteria	3	Human
Bacteria	Actinobacteria	1	Human
Eukaryota/Fungi	Ascomycota	2

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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4573570

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5459798

PDB ID

Not Available

ChEBI ID

15781

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for hercynine (MMDBc0056024)

MOL for #<Metabolite:0x00007faddef27400>

3D MOL for #<Metabolite:0x00007faddef27400>

3D SDF for #<Metabolite:0x00007faddef27400>

3D-SDF for #<Metabolite:0x00007faddef27400>

PDB for #<Metabolite:0x00007faddef27400>

3D PDB for #<Metabolite:0x00007faddef27400>

SMILES for #<Metabolite:0x00007faddef27400>

INCHI for #<Metabolite:0x00007faddef27400>

Structure for #<Metabolite:0x00007faddef27400>

3D Structure for #<Metabolite:0x00007faddef27400>