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Showing metabocard for Allicin (HMDB0033963)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:44:15 UTC
Update Date2023-02-21 17:23:49 UTC
HMDB IDHMDB0033963
Secondary Accession Numbers
  • HMDB33963
Metabolite Identification
Common NameAllicin
DescriptionAllicin belongs to the class of organic compounds known as thiosulfinic acid esters. These are organic compounds containing an ester of thiosulfinic acid with the general structure RS(=S)OR' (R, R'=alkyl, aryl). Allicin is found, on average, in the highest concentration within soft-necked garlics (Allium sativum L. var. sativum). Allicin has also been detected, but not quantified in, several different foods, such as wakames (Undaria pinnatifida), black raspberries (Rubus occidentalis), bamboo shoots (Phyllostachys edulis), spinaches (Spinacia oleracea), and chinese chestnuts (Castanea mollissima). This could make allicin a potential biomarker for the consumption of these foods. Allicin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Allicin.
Structure
Data?1677000229
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033963 (Allicin)

  Mrv0541 02241212372D          

  9  8  0  0  0  0            999 V2000
    1.7143   -0.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9821    0.1722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3123   -0.2223    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4185    0.2070    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1708   -0.1854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8204    0.2419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3123   -1.0474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5514   -0.1406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4352    0.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  8  2  0  0  0  0
  1  9  2  0  0  0  0
M  END
Download

3D MOL for HMDB0033963 (Allicin)

HMDB0033963
     RDKit          3D
Allicin
 19 18  0  0  0  0  0  0  0  0999 V2000
    4.1605    0.5452   -0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9122    0.3748    0.2856 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0876   -0.6983   -0.2973 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6087   -0.1014   -1.1140 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5579    0.7058    0.4883 S   0  0  0  0  0  4  0  0  0  0  0  0
   -0.7388    2.1230    0.1554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9648   -0.2962    0.7243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8632   -0.4142   -0.4294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -0.0218   -0.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5656   -0.1053   -0.8793 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7554    1.3395    0.3176 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4673    1.0171    1.0548 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8963   -1.4406    0.4986 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6986   -1.2216   -1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5442    0.0741    1.5990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6305   -1.3290    1.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4493   -0.8340   -1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4853    0.3876    0.5884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7933   -0.1049   -1.1863 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  3
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
M  END
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3D SDF for HMDB0033963 (Allicin)

  Mrv0541 02241212372D          

  9  8  0  0  0  0            999 V2000
    1.7143   -0.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9821    0.1722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3123   -0.2223    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4185    0.2070    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1708   -0.1854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8204    0.2419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3123   -1.0474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5514   -0.1406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4352    0.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  8  2  0  0  0  0
  1  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033963

> <DATABASE_NAME>
hmdb

> <SMILES>
C=CCSS(=O)CC=C

> <INCHI_IDENTIFIER>
InChI=1S/C6H10OS2/c1-3-5-8-9(7)6-4-2/h3-4H,1-2,5-6H2

> <INCHI_KEY>
JDLKFOPOAOFWQN-UHFFFAOYSA-N

> <FORMULA>
C6H10OS2

> <MOLECULAR_WEIGHT>
162.273

> <EXACT_MASS>
162.017306322

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
17.00941417288128

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(prop-2-ene-1-sulfinyl)sulfanyl]prop-1-ene

> <ALOGPS_LOGP>
1.16

> <JCHEM_LOGP>
2.0214

> <ALOGPS_LOGS>
-1.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-5.684360672307594

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
44.932599999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.13e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
allicin

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0033963 (Allicin)

HMDB0033963
     RDKit          3D
Allicin
 19 18  0  0  0  0  0  0  0  0999 V2000
    4.1605    0.5452   -0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9122    0.3748    0.2856 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0876   -0.6983   -0.2973 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6087   -0.1014   -1.1140 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5579    0.7058    0.4883 S   0  0  0  0  0  4  0  0  0  0  0  0
   -0.7388    2.1230    0.1554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9648   -0.2962    0.7243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8632   -0.4142   -0.4294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -0.0218   -0.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5656   -0.1053   -0.8793 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7554    1.3395    0.3176 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4673    1.0171    1.0548 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8963   -1.4406    0.4986 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6986   -1.2216   -1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5442    0.0741    1.5990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6305   -1.3290    1.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4493   -0.8340   -1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4853    0.3876    0.5884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7933   -0.1049   -1.1863 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  3
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
M  END
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PDB for HMDB0033963 (Allicin)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       3.200  -0.480   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.833   0.321   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0       0.583  -0.415   0.000  0.00  0.00           S+0
HETATM    4  S   UNK     0      -0.781   0.386   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0      -2.185  -0.346   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.398   0.452   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.583  -1.955   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -4.763  -0.262   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.546   0.269   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    8                                                       
CONECT    7    3                                                            
CONECT    8    6                                                            
CONECT    9    1                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0033963 (Allicin)

COMPND    HMDB0033963
HETATM    1  C1  UNL     1       4.161   0.545  -0.121  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.912   0.375   0.286  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.088  -0.698  -0.297  1.00  0.00           C  
HETATM    4  S1  UNL     1       0.609  -0.101  -1.114  1.00  0.00           S  
HETATM    5  S2  UNL     1      -0.558   0.706   0.488  1.00  0.00           S  
HETATM    6  O1  UNL     1      -0.739   2.123   0.155  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.965  -0.296   0.724  1.00  0.00           C  
HETATM    8  C5  UNL     1      -2.863  -0.414  -0.429  1.00  0.00           C  
HETATM    9  C6  UNL     1      -4.125  -0.022  -0.344  1.00  0.00           C  
HETATM   10  H1  UNL     1       4.566  -0.105  -0.879  1.00  0.00           H  
HETATM   11  H2  UNL     1       4.755   1.339   0.318  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.467   1.017   1.055  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.896  -1.441   0.499  1.00  0.00           H  
HETATM   14  H5  UNL     1       2.699  -1.222  -1.060  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.544   0.074   1.599  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.631  -1.329   1.035  1.00  0.00           H  
HETATM   17  H8  UNL     1      -2.449  -0.834  -1.346  1.00  0.00           H  
HETATM   18  H9  UNL     1      -4.485   0.388   0.588  1.00  0.00           H  
HETATM   19  H10 UNL     1      -4.793  -0.105  -1.186  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4   13   14
CONECT    4    5
CONECT    5    6    6    7
CONECT    7    8   15   16
CONECT    8    9    9   17
CONECT    9   18   19
END
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SMILES for HMDB0033963 (Allicin)

C=CCSS(=O)CC=C
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INCHI for HMDB0033963 (Allicin)

InChI=1S/C6H10OS2/c1-3-5-8-9(7)6-4-2/h3-4H,1-2,5-6H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H10OS2
Average Molecular Weight162.273
Monoisotopic Molecular Weight162.017306322
IUPAC Name3-[(prop-2-ene-1-sulfinyl)sulfanyl]prop-1-ene
Traditional Nameallicin
CAS Registry Number539-86-6
SMILES
C=CCSS(=O)CC=C
InChI Identifier
InChI=1S/C6H10OS2/c1-3-5-8-9(7)6-4-2/h3-4H,1-2,5-6H2
InChI KeyJDLKFOPOAOFWQN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiosulfinic acid esters. These are organic compounds containing an ester of thiosulfinic acid with the general structure RS(=S)OR' (R, R'=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassThiosulfinic acid esters
Sub ClassNot Available
Direct ParentThiosulfinic acid esters
Alternative Parents
Substituents
  • Thiosulfinic acid ester
  • Allyl sulfur compound
  • Sulfenyl compound
  • Sulfinyl compound
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point25 °CNot Available
Boiling Point248.60 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility24 mg/mL at 10 °CNot Available
LogP1.133 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB11780
Phenol Explorer Compound IDNot Available
FooDB IDFDB012190
KNApSAcK IDC00001242
Chemspider ID58548
KEGG Compound IDC07600
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAllicin
METLIN IDNot Available
PubChem Compound65036
PDB IDNot Available
ChEBI ID28411
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1009901
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Luo DQ, Guo JH, Wang FJ, Jin ZX, Cheng XL, Zhu JC, Peng CQ, Zhang C: Anti-fungal efficacy of polybutylcyanoacrylate nanoparticles of allicin and comparison with pure allicin. J Biomater Sci Polym Ed. 2009;20(1):21-31. doi: 10.1163/156856208X393473. [PubMed:19105898 ]
  2. Younis F, Mirelman D, Rabinkov A, Rosenthal T: S-allyl-mercapto-captopril: a novel compound in the treatment of Cohen-Rosenthal diabetic hypertensive rats. J Clin Hypertens (Greenwich). 2010 Jun;12(6):451-5. doi: 10.1111/j.1751-7176.2010.00270.x. [PubMed:20591093 ]
  3. Makheja AN, Bailey JM: Antiplatelet constituents of garlic and onion. Agents Actions. 1990 Mar;29(3-4):360-3. [PubMed:2111084 ]
  4. Hasan N, Siddiqui MU, Toossi Z, Khan S, Iqbal J, Islam N: Allicin-induced suppression of Mycobacterium tuberculosis 85B mRNA in human monocytes. Biochem Biophys Res Commun. 2007 Apr 6;355(2):471-6. Epub 2007 Feb 7. [PubMed:17303073 ]
  5. Park SY, Cho SJ, Kwon HC, Lee KR, Rhee DK, Pyo S: Caspase-independent cell death by allicin in human epithelial carcinoma cells: involvement of PKA. Cancer Lett. 2005 Jun 16;224(1):123-32. Epub 2004 Nov 14. [PubMed:15911108 ]
  6. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .