Hmdb loader

Showing metabocard for Homocysteine thiolactone (HMDB0002287)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:46 UTC
Update Date2023-02-21 17:16:19 UTC
HMDB IDHMDB0002287
Secondary Accession Numbers
  • HMDB02287
Metabolite Identification
Common NameHomocysteine thiolactone
DescriptionElevated level of the nonprotein amino acid homocysteine (Hcy) is a risk factor for cardiovascular diseases, neurodegenerative diseases, and neural tube defects. Metabolic conversion of Hcy to a chemically reactive metabolite, Hcy-thiolactone, catalyzed by methionyl-tRNA synthetase is the first step in a pathway that contributes to Hcy toxicity in humans. (PMID 16702349 ). The only known source of Hcy in the human body is dietary protein methionine; subsequent examinations of individual dietary amino acids have led to the conclusion that methionine, ingested in excess, is the most toxic amino acid. (Harper AE, Benevenga NJ, Wohlheuter RM. Effects of ingestion of disproportionate amounts of amino acids. Physiol Rev. 1970;50: 428 - 58; Benevenga NJ, Steele RD. Adverse effects of excessive consumption of amino acids. Annu Rev Nutr. 1984; 4:157-81). Animals fed high-protein or high-methionine diets for 2 years developed hyperhomocysteinemia and evidence of vascular disease (Fau D, Preret J, Hadjiisky P. Effects of ingestion of high protein or excess methionine diets by rats for two years. J Nutr. 1988; 118:128-33).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002287 (Homocysteine thiolactone)

  Mrv0541 02231219282D          

  7  7  0  0  0  0            999 V2000
   10.9622   -6.5887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6302   -6.1044    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   11.2165   -7.3735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2972   -6.5898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0416   -7.3742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2879   -6.4013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7848   -7.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  2  0  0  0  0
  7  3  1  0  0  0  0
M  END
Download

3D MOL for HMDB0002287 (Homocysteine thiolactone)

HMDB0002287
     RDKit          3D
Homocysteine thiolactone
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.9565   -0.1402   -0.1446 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5914    0.1829   -0.3610 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3687   -0.7862    0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7477   -0.3304   -0.2163 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5622    1.4628    0.1799 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2174    1.4709    0.2400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9295    2.3178    0.6654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4553    0.4187    0.5537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2062   -1.1307   -0.2110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3116    0.2173   -1.4529 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3686   -0.5925    1.3650 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2369   -1.8173   -0.0108 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5543   -0.7794    0.3918 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8296   -0.4937   -1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
M  END
Download

3D SDF for HMDB0002287 (Homocysteine thiolactone)

  Mrv0541 02231219282D          

  7  7  0  0  0  0            999 V2000
   10.9622   -6.5887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6302   -6.1044    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   11.2165   -7.3735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2972   -6.5898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0416   -7.3742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2879   -6.4013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7848   -7.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  2  0  0  0  0
  7  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002287

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1CCSC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H7NOS/c5-3-1-2-7-4(3)6/h3H,1-2,5H2

> <INCHI_KEY>
KIWQWJKWBHZMDT-UHFFFAOYSA-N

> <FORMULA>
C4H7NOS

> <MOLECULAR_WEIGHT>
117.169

> <EXACT_MASS>
117.024834541

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
11.432562330235712

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-aminothiolan-2-one

> <ALOGPS_LOGP>
-0.51

> <JCHEM_LOGP>
-0.250338875

> <ALOGPS_LOGS>
-0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.8258042417703395

> <JCHEM_POLAR_SURFACE_AREA>
43.09

> <JCHEM_REFRACTIVITY>
29.7591

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
DL-homocysteine thiolactone

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0002287 (Homocysteine thiolactone)

HMDB0002287
     RDKit          3D
Homocysteine thiolactone
 14 14  0  0  0  0  0  0  0  0999 V2000
   -1.9565   -0.1402   -0.1446 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5914    0.1829   -0.3610 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3687   -0.7862    0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7477   -0.3304   -0.2163 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5622    1.4628    0.1799 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2174    1.4709    0.2400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9295    2.3178    0.6654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4553    0.4187    0.5537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2062   -1.1307   -0.2110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3116    0.2173   -1.4529 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3686   -0.5925    1.3650 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2369   -1.8173   -0.0108 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5543   -0.7794    0.3918 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8296   -0.4937   -1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
M  END
Download

PDB for HMDB0002287 (Homocysteine thiolactone)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      20.463 -12.299   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0      21.710 -11.395   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0      20.937 -13.764   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      22.955 -12.301   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      22.478 -13.765   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      19.204 -11.949   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      20.132 -14.844   0.000  0.00  0.00           N+0
CONECT    1    2    3    6                                                  
CONECT    2    1    4                                                       
CONECT    3    1    5    7                                                  
CONECT    4    2    5                                                       
CONECT    5    3    4                                                       
CONECT    6    1                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
Download

3D PDB for HMDB0002287 (Homocysteine thiolactone)

COMPND    HMDB0002287
HETATM    1  N1  UNL     1      -1.957  -0.140  -0.145  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.591   0.183  -0.361  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.369  -0.786   0.288  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.748  -0.330  -0.216  1.00  0.00           C  
HETATM    5  S1  UNL     1       1.562   1.463   0.180  1.00  0.00           S  
HETATM    6  C4  UNL     1      -0.217   1.471   0.240  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.930   2.318   0.665  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.455   0.419   0.554  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.206  -1.131  -0.211  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.312   0.217  -1.453  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.369  -0.592   1.365  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.237  -1.817  -0.011  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.554  -0.779   0.392  1.00  0.00           H  
HETATM   14  H7  UNL     1       1.830  -0.494  -1.287  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3    6   10
CONECT    3    4   11   12
CONECT    4    5   13   14
CONECT    5    6
CONECT    6    7    7
END
Download

SMILES for HMDB0002287 (Homocysteine thiolactone)

NC1CCSC1=O
Download

INCHI for HMDB0002287 (Homocysteine thiolactone)

InChI=1S/C4H7NOS/c5-3-1-2-7-4(3)6/h3H,1-2,5H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
( -)-3-amino-2-ThiolanonHMDB
( -)-3-aminotetrahydro-2-ThiophenonHMDB
(+-)-3-aminodihydro-2(3H)-ThiophenoneHMDB
3-aminodihydro-2(3H)-ThiophenoneHMDB
DL-3-aminotetrahydro-2-ThiophenoneHMDB
DL-Homocysteine thiolactoneHMDB
L-Homocysteine thiolactoneHMDB
Chemical FormulaC4H7NOS
Average Molecular Weight117.169
Monoisotopic Molecular Weight117.024834541
IUPAC Name3-aminothiolan-2-one
Traditional NameDL-homocysteine thiolactone
CAS Registry Number3622-59-1
SMILES
NC1CCSC1=O
InChI Identifier
InChI=1S/C4H7NOS/c5-3-1-2-7-4(3)6/h3H,1-2,5H2
InChI KeyKIWQWJKWBHZMDT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Thiolane
  • Carbothioic s-lactone
  • Thiocarboxylic acid ester
  • Thiolactone
  • Thiocarboxylic acid or derivatives
  • Organoheterocyclic compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.00282 +/- 0.00613 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022949
KNApSAcK IDNot Available
Chemspider ID96881
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6594
PubChem Compound107712
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceTakehara, Jun; Ichikawa, Shuji; Iwane, Hiroshi. Preparation of DL-homocysteine thiolactone inorganic acid salts. Jpn. Kokai Tokkyo Koho (1998), 4 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Jakubowski H: Pathophysiological consequences of homocysteine excess. J Nutr. 2006 Jun;136(6 Suppl):1741S-1749S. [PubMed:16702349 ]
  2. Ricci G, Santoro L, Achilli M, Matarese RM, Nardini M, Cavallini D: Similarity of the oxidation products of L-cystathionine by L-amino acid oxidase to those excreted by cystathioninuric patients. J Biol Chem. 1983 Sep 10;258(17):10511-7. [PubMed:6885789 ]
  3. Jakubowski H: Homocysteine thiolactone: metabolic origin and protein homocysteinylation in humans. J Nutr. 2000 Feb;130(2S Suppl):377S-381S. [PubMed:10721911 ]
  4. Jakubowski H: Protein homocysteinylation: possible mechanism underlying pathological consequences of elevated homocysteine levels. FASEB J. 1999 Dec;13(15):2277-83. [PubMed:10593875 ]
  5. Kerkeni M, Addad F, Chauffert M, Chuniaud L, Miled A, Trivin F, Maaroufi K: Hyperhomocysteinemia, paraoxonase activity and risk of coronary artery disease. Clin Biochem. 2006 Aug;39(8):821-5. Epub 2006 Jun 7. [PubMed:16875684 ]
  6. Chwatko G, Jakubowski H: The determination of homocysteine-thiolactone in human plasma. Anal Biochem. 2005 Feb 15;337(2):271-7. [PubMed:15691507 ]