MiMeDB: Showing metabocard for Homocysteine (MMDBc0031988)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:57:40 UTC

Update Date

2022-12-15 22:51:50 UTC

Metabolite ID

MMDBc0031988

Metabolite Identification

Common Name

Homocysteine

Description

NULL

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2-Amino-4-mercaptobutyric acid	ChEBI
Hcy	ChEBI
2-Amino-4-mercaptobutyrate	Generator
(+-)-Homocysteine	HMDB
(S)-2-amino-4-mercapto-Butanoate	HMDB
(S)-2-amino-4-mercapto-Butanoic acid	HMDB
2-amino-4-mercapto-Butanoate	HMDB
2-amino-4-mercapto-Butanoic acid	HMDB
2-amino-4-mercapto-Butyric acid	HMDB
2-amino-4-mercapto-DL-Butyrate	HMDB
2-amino-4-mercapto-DL-Butyric acid	HMDB
2-amino-4-Sulfanylbutanoate	HMDB
2-amino-4-Sulfanylbutanoic acid	HMDB
D,L-Homocysteine	HMDB
DL-2-amino-4-mercapto-Butyric acid	HMDB
DL-2-amino-4-Mercaptobutyric acid	HMDB
DL-Homocysteine	HMDB
DL-Homocysteine (free base)	HMDB
homo-CYS	HMDB
L-2-amino-4-mercapto-Butyric acid	HMDB
L-Homocysteine	HMDB
Usaf b-12	HMDB
Homocysteine, L isomer	MeSH, HMDB
Homocysteine, L-isomer	MeSH, HMDB
2 amino 4 Mercaptobutyric acid	MeSH, HMDB
L-Isomer homocysteine	MeSH, HMDB

Molecular Formula

C₄H₉NO₂S

Average Mass

135.185

Monoisotopic Mass

135.035399227

IUPAC Name

2-amino-4-sulfanylbutanoic acid

Traditional Name

homocysteine

CAS Registry Number

Not Available

SMILES

NC(CCS)C(O)=O

InChI Identifier

InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)

InChI Key

FFFHZYDWPBMWHY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids

Alternative Parents

Substituents

Alpha-amino acid
Thia fatty acid
Fatty acyl
Fatty acid
Amino acid
Alkylthiol
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Hydrocarbon derivative
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic oxide
Primary aliphatic amine
Organopnictogen compound
Carbonyl group
Amine
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

sulfur-containing amino acid (CHEBI:17230 )
non-proteinogenic alpha-amino acid (CHEBI:17230 )
homocysteines (CHEBI:17230 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	14.8 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.6	ChemAxon
logS	-0.96	ALOGPS
pKa (Strongest Acidic)	2.46	ChemAxon
pKa (Strongest Basic)	9.41	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	32.94 m³·mol⁻¹	ChemAxon
Polarizability	13.44 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Adipose Tissue
Brain
Feces
Fibroblasts
Intestine
Kidney
Liver
Neuron
Pancreas
Placenta
Platelet
Skeletal Muscle

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	Proteobacteria	174	Human feces; Human sputum; Human ; Human unknown; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Pig	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	119	Human feces; Human ; Human pleural fluid plaque; Human dental plaque; Human sputum; Human nasopharyngeal swab	Metabolic reconstruction
Bacteria	Firmicutes	365	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	116	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces	Unknown

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Adipose Tissue	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Brain	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Intestine	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Kidney	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Neuron	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Pancreas	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Platelet	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Skeletal Muscle	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001491

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C05330

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Homocysteine

METLIN ID

Not Available

PubChem Compound

778

PDB ID

Not Available

ChEBI ID

17230

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Sunden SL, Renduchintala MS, Park EI, Miklasz SD, Garrow TA: Betaine-homocysteine methyltransferase expression in porcine and human tissues and chromosomal localization of the human gene. Arch Biochem Biophys. 1997 Sep 1;345(1):171-4. doi: 10.1006/abbi.1997.0246. [PubMed:9281325 ]
Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for Homocysteine (MMDBc0031988)

MOL for #<Metabolite:0x0000560bdef367f0>

3D MOL for #<Metabolite:0x0000560bdef367f0>

3D SDF for #<Metabolite:0x0000560bdef367f0>

3D-SDF for #<Metabolite:0x0000560bdef367f0>

PDB for #<Metabolite:0x0000560bdef367f0>

3D PDB for #<Metabolite:0x0000560bdef367f0>

SMILES for #<Metabolite:0x0000560bdef367f0>

INCHI for #<Metabolite:0x0000560bdef367f0>

Structure for #<Metabolite:0x0000560bdef367f0>

3D Structure for #<Metabolite:0x0000560bdef367f0>