L-Homocysteine (PAMDB000067)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000067
Identification
Name: L-Homocysteine
Description:Homocysteine is a thiol-containing amino acid formed by a demethylation of methionine. Homocysteine is a variant of the amino acid cysteine, differing in that its side-chain contains an additional methylene (-CH2-) group before the thiol (-SH) group. In Pseudomonas aeruginosa homocysteine (Hcy) is the last intermediate on the methionine biosynthetic pathway.
Structure
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🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • (+-)-homocysteine
  • (S)-2-amino-4-mercapto-Butanoate
  • (S)-2-amino-4-mercapto-Butanoic acid
  • (S)-2-Amino-4-mercaptobutanoate
  • (S)-2-Amino-4-mercaptobutanoic acid
  • (S)-Homocysteine
  • 2-amino-4-mercapto-Butanoate
  • 2-amino-4-mercapto-Butanoic acid
  • 2-Amino-4-mercapto-Butyrate
  • 2-Amino-4-mercapto-Butyric acid
  • 2-amino-4-mercapto-DL-Butyrate
  • 2-amino-4-mercapto-DL-Butyric acid
  • 2-Amino-4-mercapto-L-butyrate
  • 2-Amino-4-mercapto-L-butyric acid
  • 2-Amino-4-mercaptobutyrate
  • 2-Amino-4-mercaptobutyric acid
  • 2-amino-4-sulfanylbutanoate
  • 2-amino-4-sulfanylbutanoic acid
  • 2-amino-4-Sulphanylbutanoate
  • 2-amino-4-Sulphanylbutanoic acid
  • D,l-homocysteine
  • DL-2-amino-4-mercapto-Butyrate
  • DL-2-amino-4-mercapto-Butyric acid
  • DL-2-amino-4-Mercaptobutyrate
  • DL-2-Amino-4-mercaptobutyric acid
  • DL-Homocysteine
  • DL-homocysteine (free base)
  • HCY
  • Homo-cys
  • Homocysteine
  • L-2-Amino-4-mercapto-Butyrate
  • L-2-Amino-4-mercapto-Butyric acid
  • L-2-Amino-4-mercaptobutyrate
  • L-2-Amino-4-mercaptobutyric acid
  • L-Homocysteine
  • Usaf B-12
Chemical Formula: C4H9NO2S
Average Molecular Weight: 135.185
Monoisotopic Molecular Weight: 135.035399227
InChI Key: FFFHZYDWPBMWHY-VKHMYHEASA-N
InChI:InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1
CAS number: 6027-13-0
IUPAC Name:(2S)-2-amino-4-sulfanylbutanoic acid
Traditional IUPAC Name: L-homocysteine
SMILES:N[C@@H](CCS)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound 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 ClassOrganic acids and derivatives
Class Carboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct Parent L-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Thia fatty acid
  • Amino fatty acid
  • Fatty acyl
  • Fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Alkylthiol
  • Hydrocarbon derivative
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 232.6 °C
Experimental Properties:
PropertyValueSource
LogP:-2.538PhysProp
Predicted Properties
PropertyValueSource
Water Solubility14.8 mg/mLALOGPS
logP-2.3ALOGPS
logP-2.6ChemAxon
logS-0.96ALOGPS
pKa (Strongest Acidic)2.46ChemAxon
pKa (Strongest Basic)9.41ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area63.32 Å2ChemAxon
Rotatable Bond Count3ChemAxon
Refractivity32.93 m3·mol-1ChemAxon
Polarizability13.54 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
L-Cystathionine + Water > L-Homocysteine + Ammonium + Pyruvic acid
5-Methyltetrahydrofolic acid + L-Homocysteine <> Hydrogen ion + L-Methionine + Tetrahydrofolic acid
L-Homocysteine + S-Methylmethionine > Hydrogen ion +2 L-Methionine
S-Adenosylmethionine + L-Homocysteine + S-Methylmethionine <> S-Adenosylhomocysteine + Hydrogen ion + L-Methionine
S-Ribosyl-L-homocysteine > 4,5-Dihydroxy-2,3-pentanedione + L-Homocysteine
S-Adenosylmethionine + L-Homocysteine <> S-Adenosylhomocysteine + L-Methionine
5-Methyltetrahydrofolic acid + L-Homocysteine <> Tetrahydrofolic acid + L-Methionine
Cystathionine + Water <> L-Homocysteine + Ammonia + Pyruvic acid
L-Cystathionine + Water <> L-Homocysteine + Ammonia + Pyruvic acid
O-Succinyl-L-homoserine + Hydrogen sulfide <> L-Homocysteine + Succinic acid
S-Ribosyl-L-homocysteine <> (4S)-4,5-Dihydroxypentan-2,3-dione + L-Homocysteine
5-Methyltetrahydropteroyltri-L-glutamic acid + L-Homocysteine <> Tetrahydropteroyltri-L-glutamic acid + L-Methionine
L-Cystathionine + Water > Hydrogen ion + Pyruvic acid + Ammonia + L-Homocysteine
L-Homocysteine + 5-Methyltetrahydropteroyltri-L-glutamic acid > L-Methionine + tetrahydropteroyl tri-L-glutamate
L-Homocysteine + S-Adenosylmethionine Hydrogen ion + L-Methionine + S-Adenosylhomocysteine
S-methyl-L-methionine + L-Homocysteine Hydrogen ion + L-Methionine
5-methyltetrahydropteroyltri-L-glutamate + L-Homocysteine > tetrahydropteroyltri-L-glutamate + L-Methionine
L-Cystathionine + Water + 2-Aminoacrylic acid + 2-Iminopropanoate <> L-Homocysteine + Pyruvic acid + Ammonia
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MSNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00ko-9800000000-80a1c80328e8836233a4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-9100000000-1f611da44349ffdfaefeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0bvi-9000000000-c9d62a66522e46a17f56View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-3900000000-e8322d5858cba16a3bd2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00lr-6900000000-e0190a1cc33e605bac0aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-9000000000-900bb5d8fb11bec02e39View in MoNA
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Biochem Prepn. 5 93 (1957)
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID17588
HMDB IDHMDB00742
Pubchem Compound ID91552
Kegg IDC00155
ChemSpider ID82666
WikipediaHomocysteine
BioCyc IDHOMO-CYS
EcoCyc IDHOMO-CYS
Ligand ExpoHCS