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L-Homocysteine

PubChem CID
91552
Structure
L-Homocysteine_small.png
L-Homocysteine_3D_Structure.png
Molecular Formula
Synonyms
  • L-Homocysteine
  • homocysteine
  • 6027-13-0
  • (2S)-2-amino-4-sulfanylbutanoic acid
  • (s)-2-amino-4-mercaptobutanoic acid
Molecular Weight
135.19 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-01-18
Description
L-homocysteine is a homocysteine that has L configuration. It has a role as a mouse metabolite. It is a homocysteine and a serine family amino acid. It is a conjugate acid of a L-homocysteinate. It is a tautomer of a L-homocysteine zwitterion.
Homocysteine is a thiol-containing amino acid formed by a demethylation of methionine.
L-Homocysteine is a metabolite found in or produced by Escherichia coli (strain K12, MG1655).

1 Structures

1.1 2D Structure

Chemical Structure Depiction
L-Homocysteine.png

1.2 3D Conformer

2 Biologic Description

SVG Image
SVG Image
IUPAC Condensed
H-Hcy-OH
Sequence
X
HELM
PEPTIDE1{[Hcy]}$$$$
IUPAC
L-homocysteine

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

(2S)-2-amino-4-sulfanylbutanoic acid
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

FFFHZYDWPBMWHY-VKHMYHEASA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

C(CS)[C@@H](C(=O)O)N
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C4H9NO2S
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

3.3.2 Deprecated CAS

454-28-4

3.3.3 European Community (EC) Number

3.3.4 UNII

3.3.5 ChEBI ID

3.3.6 ChEMBL ID

3.3.7 DrugBank ID

3.3.8 DSSTox Substance ID

3.3.9 HMDB ID

3.3.10 KEGG ID

3.3.11 Metabolomics Workbench ID

3.3.12 NCI Thesaurus Code

3.3.13 Nikkaji Number

3.3.14 Wikidata

3.3.15 Wikipedia

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • 2 amino 4 mercaptobutyric acid
  • 2-amino-4-mercaptobutyric acid
  • Homocysteine
  • Homocysteine, L Isomer
  • Homocysteine, L-Isomer
  • L-Isomer Homocysteine

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
135.19 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3
Property Value
-3.4
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
135.03539970 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
135.03539970 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
64.3 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
8
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
86.1
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
1
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

4.2 Experimental Properties

4.2.1 Physical Description

Solid

4.2.2 Melting Point

232 - 233 °C

4.2.3 Solubility

148 mg/mL

4.2.4 Dissociation Constants

4.2.5 Collision Cross Section

130.53 Ų [M+H]+ [CCS Type: DT; Method: stepped-field]

159.62 Ų [M-H]- [CCS Type: DT; Method: stepped-field]

127.6 Ų [M+Na-2H]- [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

130.3 Ų [M+H]+ [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

143.6 Ų [M-H]- [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

124 Ų [M+H]+ [CCS Type: TW; Method: calibrated with polyalanine]

4.3 Chemical Classes

4.3.1 Drugs

Pharmaceuticals -> Metabolite of Erdosteine
S113 | SWISSPHARMA24 | 2024 Swiss Pharmaceutical List with Metabolites | DOI:10.5281/zenodo.10501043
Pharmaceuticals -> Listed in ZINC15
S55 | ZINC15PHARMA | Pharmaceuticals from ZINC15 | DOI:10.5281/zenodo.3247749

5 Spectral Information

5.1 1D NMR Spectra

5.1.1 1H NMR Spectra

1 of 3
View All
Spectra ID
Instrument Type
Varian
Frequency
500 MHz
Solvent
Water
pH
7.00
Shifts [ppm]:Intensity
2.65:81.39, 2.69:22.39, 2.12:78.36, 2.68:80.71, 2.13:71.60, 3.87:81.02, 2.15:48.91, 2.62:29.70, 2.17:55.08, 2.66:85.79, 2.16:48.60, 2.64:100.00, 3.87:85.13, 3.88:71.97, 2.67:83.64, 2.17:62.47, 2.18:55.14, 2.63:79.86, 3.86:71.52, 2.09:20.51, 2.15:65.22, 2.15:54.61, 2.19:20.14, 2.60:23.83, 2.71:19.54, 2.14:46.86, 2.10:58.49, 2.64:97.73, 2.69:25.96, 2.21:14.60, 2.07:13.18, 2.66:74.70
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2 of 3
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Spectra ID
Instrument Type
JEOL
Frequency
400 MHz
Solvent
D2O
Shifts [ppm]:Intensity
2.15:428.00, 2.63:508.00, 2.24:81.00, 2.22:110.00, 2.10:118.00, 2.67:1000.00, 2.21:132.00, 2.17:327.00, 2.12:327.00, 2.15:333.00, 2.71:167.00, 2.71:164.00, 2.69:490.00, 2.22:122.00, 2.10:98.00, 3.88:631.00, 2.08:65.00, 2.19:344.00, 2.66:812.00, 3.91:611.00, 2.17:377.00, 2.14:475.00, 3.89:803.00, 2.65:739.00, 2.22:102.00, 2.62:135.00, 3.89:693.00, 2.20:343.00, 2.60:123.00, 2.15:446.00, 2.17:382.00, 2.18:379.00, 2.62:167.00, 2.16:352.00, 2.73:119.00, 2.18:395.00, 2.68:582.00
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5.1.2 13C NMR Spectra

Spectra ID
Instrument Type
Bruker
Solvent
D2O
pH
7.4
Shifts [ppm]:Intensity
22.51:78.08, 37.40:88.33, 177.09:31.30, 56.34:102.72
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5.2 2D NMR Spectra

5.2.1 1H-13C NMR Spectra

2D NMR Spectra Type
1H-13C HSQC
Spectra ID
Instrument Type
Bruker
Frequency
600 MHz
Solvent
Water
pH
7.00
Shifts [ppm] (F2:F1):Intensity
3.87:56.41:1.00, 2.66:22.57:0.73, 2.15:37.35:0.49
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5.3 Mass Spectrometry

5.3.1 GC-MS

1 of 4
View All
Spectra ID
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

128.0 100

160.0 38.04

278.0 23.72

100.0 17.72

147.0 15.72

Thumbnail
Thumbnail
Notes
instrument=Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies
2 of 4
View All
MoNA ID
MS Category
Experimental
MS Type
GC-MS
MS Level
MS1
Instrument
Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Retention Time
1130.49 sec
Top 5 Peaks

128 100

160 38.04

278 23.72

100 17.72

147 15.72

Thumbnail
Thumbnail
License
CC BY-SA

5.3.2 MS-MS

1 of 6
View All
Spectra ID
Ionization Mode
Positive
Top 5 Peaks

136.01956 100

107.05154 85.71

Thumbnail
Thumbnail
2 of 6
View All
Spectra ID
Instrument Type
LC-ESI-ITFT
Ionization Mode
positive
Top 5 Peaks

118.009033 100

90.006973 51.38

56.050495 0.36

119.035492 0.12

102.143936 0.06

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Notes
instrument=LTQ Orbitrap XL, Thermo Scientfic

5.3.3 LC-MS

1 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
LC-MS
MS Level
MS1
Instrument
LTQ Orbitrap XL, Thermo Scientfic
Instrument Type
LC-ESI-ITFT
Ionization
ESI
Ionization Mode
positive
Collision Energy
35eV
Retention Time
5.475585 min
Top 5 Peaks

136.042632 100

269.062817 17.64

118.032020 9.63

148.042615 7.81

137.045596 4.75

Thumbnail
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License
CC BY-SA
2 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
136.04
Instrument
LTQ Orbitrap XL, Thermo Scientfic
Instrument Type
LC-ESI-ITFT
Ionization
ESI
Ionization Mode
positive
Collision Energy
35eV
Retention Time
5.483193 min
Top 5 Peaks

117.943787 100

90.004913 49.80

56.056892 0.44

118.939880 0.13

112.948395 0.09

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License
CC BY-SA

7 Chemical Vendors

8 Drug and Medication Information

8.1 Biomarker Information

9 Pharmacology and Biochemistry

9.1 Human Metabolite Information

9.1.1 Tissue Locations

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

9.1.2 Cellular Locations

Cytoplasm

9.1.3 Metabolite Pathways

9.2 Biochemical Reactions

10 Safety and Hazards

10.1 Hazards Identification

10.1.1 GHS Classification

Note
Pictograms displayed are for 97.5% (39 of 40) of reports that indicate hazard statements. This chemical does not meet GHS hazard criteria for 2.5% (1 of 40) of reports.
Pictogram(s)
Irritant
Signal
Warning
GHS Hazard Statements
H302 (97.5%): Harmful if swallowed [Warning Acute toxicity, oral]
Precautionary Statement Codes

P264, P270, P301+P317, P330, and P501

(The corresponding statement to each P-code can be found at the GHS Classification page.)

ECHA C&L Notifications Summary

Aggregated GHS information provided per 40 reports by companies from 2 notifications to the ECHA C&L Inventory.

Reported as not meeting GHS hazard criteria per 1 of 40 reports by companies. For more detailed information, please visit ECHA C&L website.

There is 1 notification provided by 39 of 40 reports by companies with hazard statement code(s).

Information may vary between notifications depending on impurities, additives, and other factors. The percentage value in parenthesis indicates the notified classification ratio from companies that provide hazard codes. Only hazard codes with percentage values above 10% are shown.

10.1.2 Hazard Classes and Categories

Acute Tox. 4 (97.5%)

11 Toxicity

11.1 Toxicological Information

11.1.1 Acute Effects

12 Associated Disorders and Diseases

Disease
Creutzfeldt-Jakob disease
References
Disease
Sickle cell anemia
References
Disease
Stroke
References
Disease
Peripheral neuropathy
References
Disease
Chronic renal failure
References
Disease
Continuous ambulatory peritoneal dialysis
References
Disease
Homocystinuria
References

PubMed: 14264314, 8745393

MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de)

Disease
Amyotrophic lateral sclerosis
References
Disease
Progressive supranuclear palsy
References
PubMed: 20606437
Disease
Uremia
References

PubMed: 11865086, 10509899, 9607216, 7482520, 6520173, 22626821, 21359215, 2026685, 9573551, 24023812, 15353324, 19309105, 8087979, 17132244, 12675874

Merck Manual of Diagnosis and Therapy.

David F. Putnam Composition and Concentrative Properties of Human Urine. NASA Contractor Report. July 1971

Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.

Geigy Scientific Tables, 8th Rev edition, pp. 165-177. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.

National Health and Nutrition Examination Survey (NHANES Survey) 2013

Geigy Scientific Tables, 8th Rev edition, pp. 80-82. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.

Disease
Sulfite oxidase deficiency, ISOLATED
References

PubMed: 10682307, 27289259, 23452914, 15558695

Clinical and Laboratory Barriers to the Timely Diagnosis of Sulphite Oxidase Deficiency. Proceedings of Singapore Healthcare, 19(2), 94-100.

Disease
Methylenetetrahydrofolate reductase deficiency
References

PubMed: 8456826

MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de)

Disease
Molybdenum cofactor deficiency
References

PubMed: 10102915, 12872846, 27289259, 8051926

MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de)

Disease
Cystathioninuria
References

PubMed: 1429979, 20584029

MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de)

Disease
Molybdenium co-factor deficiency
References
Disease
Dimethylglycine Dehydrogenase Deficiency
References
PubMed: 10102904
Disease
Dementia
References
Disease
Colorectal cancer
References

PubMed: 7482520, 19006102, 23940645, 24424155, 20156336, 19678709, 22148915, 25105552, 21773981, 25037050, 27015276, 27107423, 27275383, 28587349

Silke Matysik, Caroline Ivanne Le Roy, Gerhard Liebisch, Sandrine Paule Claus. Metabolomics of fecal samples: A practical consideration. Trends in Food Science & Technology. Vol. 57, Part B, Nov. 2016, p.244-255: http://www.sciencedirect.com/science/article/pii/S0924224416301984

Disease
Transcobalamin II deficiency
References
PubMed: 10518276

13 Literature

13.1 Consolidated References

13.2 NLM Curated PubMed Citations

13.3 Springer Nature References

13.4 Wiley References

13.5 Nature Journal References

13.6 Chemical Co-Occurrences in Literature

13.7 Chemical-Gene Co-Occurrences in Literature

13.8 Chemical-Disease Co-Occurrences in Literature

14 Patents

14.1 Depositor-Supplied Patent Identifiers

14.2 WIPO PATENTSCOPE

14.3 Chemical Co-Occurrences in Patents

14.4 Chemical-Disease Co-Occurrences in Patents

14.5 Chemical-Gene Co-Occurrences in Patents

15 Interactions and Pathways

15.1 Protein Bound 3D Structures

15.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

15.2 Chemical-Target Interactions

15.3 Pathways

16 Biological Test Results

16.1 BioAssay Results

17 Taxonomy

Zebrafish Pathway Metabolite MetFrag Local CSV (Beta) | DOI:10.5281/zenodo.3457553
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

18 Classification

18.1 MeSH Tree

18.2 NCI Thesaurus Tree

18.3 ChEBI Ontology

18.4 KEGG: Metabolite

18.5 ChemIDplus

18.6 ChEMBL Target Tree

18.7 UN GHS Classification

18.8 NORMAN Suspect List Exchange Classification

18.9 CCSBase Classification

18.10 EPA DSSTox Classification

18.11 LOTUS Tree

18.12 EPA Substance Registry Services Tree

18.13 MolGenie Organic Chemistry Ontology

19 Information Sources

  1. CAS Common Chemistry
    LICENSE
    The data from CAS Common Chemistry is provided under a CC-BY-NC 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc/4.0/
  2. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. DrugBank
    LICENSE
    Creative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)
    https://www.drugbank.ca/legal/terms_of_use
  4. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  5. European Chemicals Agency (ECHA)
    LICENSE
    Use of the information, documents and data from the ECHA website is subject to the terms and conditions of this Legal Notice, and subject to other binding limitations provided for under applicable law, the information, documents and data made available on the ECHA website may be reproduced, distributed and/or used, totally or in part, for non-commercial purposes provided that ECHA is acknowledged as the source: "Source: European Chemicals Agency, http://echa.europa.eu/". Such acknowledgement must be included in each copy of the material. ECHA permits and encourages organisations and individuals to create links to the ECHA website under the following cumulative conditions: Links can only be made to webpages that provide a link to the Legal Notice page.
    https://echa.europa.eu/web/guest/legal-notice
  6. FDA Global Substance Registration System (GSRS)
    LICENSE
    Unless otherwise noted, the contents of the FDA website (www.fda.gov), both text and graphics, are not copyrighted. They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA. Credit to the U.S. Food and Drug Administration as the source is appreciated but not required.
    https://www.fda.gov/about-fda/about-website/website-policies#linking
  7. Human Metabolome Database (HMDB)
    LICENSE
    HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
    http://www.hmdb.ca/citing
  8. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  9. ChEBI
  10. E. coli Metabolome Database (ECMDB)
    LICENSE
    ECMDB is offered to the public as a freely available resource.
    https://ecmdb.ca/citations
  11. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  12. NCI Thesaurus (NCIt)
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  13. ChEMBL
    LICENSE
    Access to the web interface of ChEMBL is made under the EBI's Terms of Use (http://www.ebi.ac.uk/Information/termsofuse.html). The ChEMBL data is made available on a Creative Commons Attribution-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-sa/3.0/).
    http://www.ebi.ac.uk/Information/termsofuse.html
  14. ECI Group, LCSB, University of Luxembourg
    LICENSE
    Data: CC-BY 4.0; Code: Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    Homocysteine
  15. Natural Product Activity and Species Source (NPASS)
  16. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  17. IUPAC Digitized pKa Dataset
  18. Japan Chemical Substance Dictionary (Nikkaji)
  19. KEGG
    LICENSE
    Academic users may freely use the KEGG website. Non-academic use of KEGG generally requires a commercial license
    https://www.kegg.jp/kegg/legal.html
  20. MarkerDB
    LICENSE
    This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
    https://markerdb.ca/
  21. Metabolomics Workbench
  22. Nature Chemical Biology
  23. NORMAN Suspect List Exchange
    LICENSE
    Data: CC-BY 4.0; Code (hosted by ECI, LCSB): Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    Homocystein
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  24. Protein Data Bank in Europe (PDBe)
  25. RCSB Protein Data Bank (RCSB PDB)
    LICENSE
    Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data.
    https://www.rcsb.org/pages/policies
  26. Springer Nature
  27. Wikidata
  28. Wikipedia
  29. Wiley
  30. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
  31. PubChem
  32. GHS Classification (UNECE)
  33. EPA Substance Registry Services
  34. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  35. PATENTSCOPE (WIPO)
  36. NCBI
CONTENTS