Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:46:40 UTC
Update Date2021-09-26 22:56:03 UTC
HMDB IDHMDB0246764
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-(delta-Carboxybutyl)homocysteine
Description5-(delta-Carboxybutyl)homocysteine 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). Based on a literature review a small amount of articles have been published on 5-(delta-Carboxybutyl)homocysteine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-(delta-carboxybutyl)homocysteine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-(delta-Carboxybutyl)homocysteine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
5-(Δ-carboxybutyl)homocysteineGenerator
S-(alpha-Carboxybutyl)-DL-homocysteineHMDB
Chemical FormulaC8H15NO4S
Average Molecular Weight221.27
Monoisotopic Molecular Weight221.072179141
IUPAC Name2-amino-4-[(3-carboxypropyl)sulfanyl]butanoic acid
Traditional Name2-amino-4-[(3-carboxypropyl)sulfanyl]butanoic acid
CAS Registry NumberNot Available
SMILES
NC(CCSCCCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C8H15NO4S/c9-6(8(12)13)3-5-14-4-1-2-7(10)11/h6H,1-5,9H2,(H,10,11)(H,12,13)
InChI KeyGAWAENRCVHPTKZ-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).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Thia fatty acid
  • Dicarboxylic acid or derivatives
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Carboxylic acid
  • Thioether
  • Sulfenyl compound
  • Dialkylthioether
  • Organic oxygen compound
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organic oxide
  • Amine
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-2.3ALOGPS
logP-2.3ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)2.07ChemAxon
pKa (Strongest Basic)9.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area100.62 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity53.17 m³·mol⁻¹ChemAxon
Polarizability23.09 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+143.36830932474
DeepCCS[M-H]-139.34830932474
DeepCCS[M-2H]-177.23330932474
DeepCCS[M+Na]+152.8130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-(delta-Carboxybutyl)homocysteineNC(CCSCCCC(O)=O)C(O)=O3170.7Standard polar33892256
5-(delta-Carboxybutyl)homocysteineNC(CCSCCCC(O)=O)C(O)=O1788.4Standard non polar33892256
5-(delta-Carboxybutyl)homocysteineNC(CCSCCCC(O)=O)C(O)=O2162.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #1C[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C2172.0Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #1C[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C2150.2Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #1C[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C2395.7Standard polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #2C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2290.8Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #2C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2208.4Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #2C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C2597.0Standard polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #3C[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C2310.9Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #3C[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C2185.5Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #3C[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C2572.2Standard polar33892256
5-(delta-Carboxybutyl)homocysteine,4TMS,isomer #1C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2310.1Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,4TMS,isomer #1C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2263.5Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,4TMS,isomer #1C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C2288.0Standard polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2849.6Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2728.6Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2710.3Standard polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2972.6Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2764.1Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2813.2Standard polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2982.4Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2751.3Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2804.7Standard polar33892256
5-(delta-Carboxybutyl)homocysteine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3203.8Semi standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2980.5Standard non polar33892256
5-(delta-Carboxybutyl)homocysteine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2708.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (Non-derivatized) - 70eV, Positivesplash10-009f-9300000000-9a8e170cde019b0474bc2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 10V, Positive-QTOFsplash10-0fk9-2490000000-eb0f0634284ac231cdfc2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 20V, Positive-QTOFsplash10-052r-9200000000-b6c8484f179243b403b02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 40V, Positive-QTOFsplash10-052u-9000000000-5752504976ab0251f7922021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 10V, Negative-QTOFsplash10-01b9-0940000000-6e6ed0d4f8111841ca332021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 20V, Negative-QTOFsplash10-0uxr-0900000000-d03333e6ad4e06e625822021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 40V, Negative-QTOFsplash10-0f89-9300000000-1b6ea354a4b5d5825d1f2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID23272411
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44413151
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]