Bovine Metabolome Database: Showing metabocard for Homocysteine (BMDB0000742)

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Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (6) Show 6 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:35:50 UTC

Update Date

2020-05-21 16:28:33 UTC

BMDB ID

BMDB0000742

Secondary Accession Numbers

BMDB00742

Metabolite Identification

Common Name

Homocysteine

Description

Homocysteine, also known as Hcy or homo-cys, 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). Homocysteine exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule. Homocysteine exists in all living species, ranging from bacteria to humans. Homocysteine is a potentially toxic compound.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
Hcy	ChEBI
L-2-Amino-4-mercaptobutyric acid	ChEBI
L-2-Amino-4-mercaptobutyrate	Generator
2-Amino-4-mercaptobutyric acid	HMDB
Homocysteine, L isomer	HMDB
L-Isomer homocysteine	HMDB
2 Amino 4 mercaptobutyric acid	HMDB
Homocysteine, L-isomer	HMDB
(S)-2-Amino-4-mercapto-butanoate	HMDB
(S)-2-Amino-4-mercapto-butanoic acid	HMDB
(S)-2-Amino-4-mercaptobutanoic acid	HMDB
(S)-Homocysteine	HMDB
2-Amino-4-mercapto-DL-butyrate	HMDB
2-Amino-4-mercapto-DL-butyric acid	HMDB
2-Amino-4-mercapto-L-butyric 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-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
Homo-cys	HMDB
L-2-Amino-4-mercapto-butyric acid	HMDB
L-Homocysteine	HMDB
2-Amino-4-mercapto-butyrate	HMDB
Homocysteine	MeSH, KEGG

Chemical Formula

C₄H₉NO₂S

Average Molecular Weight

135.185

Monoisotopic Molecular Weight

135.035399227

IUPAC Name

(2S)-2-amino-4-sulfanylbutanoic acid

Traditional Name

L-homocysteine

CAS Registry Number

454-29-5

SMILES

N[C@@H](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)/t3-/m0/s1

InChI Key

FFFHZYDWPBMWHY-VKHMYHEASA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

homocysteine (CHEBI:17588 )
serine family amino acid (CHEBI:17588 )
Other amino acids (C00155 )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	232 - 233 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	148 mg/mL	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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	13.54 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-004i-0920000000-20fbffbe76510c066e6f	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9000000000-1f800d28bca4b2b7a49f	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-014l-4900000000-c50d79ba3a5013bcf29f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-000i-9000000000-025c9e1f4fb58138c43b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-014i-4900000000-33f205e002f49f034764	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-052r-0900000000-c1f98c8182b5ddc09cb1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00ko-9800000000-80a1c80328e8836233a4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-9100000000-1f611da44349ffdfaefe	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0bvi-9000000000-c9d62a66522e46a17f56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-3900000000-e8322d5858cba16a3bd2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00lr-6900000000-e0190a1cc33e605bac0a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9000000000-900bb5d8fb11bec02e39	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0900000000-38e427e24202b2411597	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-7900000000-5cf2133d9faac56032d3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9000000000-942ac689538269d6ca7b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-9000000000-166428542631f9ac0714	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-9000000000-9bcb57b924579a6c3411	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4j-9000000000-8eee886864db64f3eec2	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, D₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

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

Pathways

Name	SMPDB/Pathwhiz	KEGG
Betaine Metabolism		Not Available
Homocysteine Degradation		Not Available
Glycine and Serine Metabolism		Not Available
Methionine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Adipose Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Brain	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 29565828	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Pancreas	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000742

DrugBank ID

DB04422

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Homocysteine

METLIN ID

3256

PubChem Compound

91552

PDB ID

Not Available

ChEBI ID

17588

References

Synthesis Reference

Karrenbauer, Michael; Kleemann, Axel; Luessling, Theodor; Schaefer, Fritz. D,L-Homocysteine (I). Ger. (1984), 4 pp.

Material Safety Data Sheet (MSDS)

Not Available

General References

Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]

Enzymes

Enzyme Details

1. Methionine synthase

General function:: Amino acid transport and metabolism
Specific function:: Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity).
Gene Name:: MTR
Uniprot ID:: Q4JIJ3
Molecular weight:: 140478.0

Reactions

Homocysteine + 5-Methyltetrahydrofolic acid → L-Methionine + Tetrahydrofolic acid	details

Enzyme Details

2. Adenosylhomocysteinase

General function:: Coenzyme transport and metabolism
Specific function:: Not Available
Gene Name:: AHCYL1
Uniprot ID:: A5PKK6
Molecular weight:: 68585.0

Enzyme Details

3. Adenosylhomocysteinase 3

General function:: Coenzyme transport and metabolism
Specific function:: May regulate the electrogenic sodium/bicarbonate cotransporter SLC4A4 activity and Mg(2+)-sensitivity. On the contrary of its homolog AHCYL1, does not regulate ITPR1 sensitivity to inositol 1,4,5-trisphosphate (By similarity).
Gene Name:: AHCYL2
Uniprot ID:: A6QLP2
Molecular weight:: 66774.0

Enzyme Details

4. Betaine--homocysteine S-methyltransferase 1

General function:: Amino acid transport and metabolism
Specific function:: Involved in the regulation of homocysteine metabolism. Converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline (By similarity).
Gene Name:: BHMT
Uniprot ID:: Q5I597
Molecular weight:: 44878.0

Reactions

Betaine + Homocysteine → Dimethylglycine + L-Methionine	details
L-Cystathionine → Homocysteine	details

Enzyme Details

5. Adenosylhomocysteinase

General function:: Coenzyme transport and metabolism
Specific function:: Adenosylhomocysteine is a competitive inhibitor of S-adenosyl-L-methionine-dependent methyl transferase reactions; therefore adenosylhomocysteinase may play a key role in the control of methylations via regulation of the intracellular concentration of adenosylhomocysteine.
Gene Name:: AHCY
Uniprot ID:: Q3MHL4
Molecular weight:: 47638.0

Reactions

S-Adenosylhomocysteine + Water → Homocysteine + Adenosine	details

Enzyme Details

6. Cystathionine beta-synthase

General function:: Not Available
Specific function:: Not Available
Gene Name:: CBS
Uniprot ID:: F1MEW4
Molecular weight:: 62867.0

Reactions

Homocysteine + L-Serine → Water + L-Cystathionine	details

Showing metabocard for Homocysteine (BMDB0000742)

Structure for BMDB0000742 (Homocysteine)

Enzymes

Reactions

Reactions

Reactions

Reactions