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Showing metabocard for Heliotridine (HMDB0253071)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:14:36 UTC
Update Date2021-09-26 23:06:04 UTC
HMDB IDHMDB0253071
Secondary Accession NumbersNone
Metabolite Identification
Common NameHeliotridine
Description7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-ol belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus. Based on a literature review very few articles have been published on 7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-ol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Heliotridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Heliotridine 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0253071 (Heliotridine)

  Mrv1533004171501502D          

 11 12  0  0  0  0            999 V2000
    0.2076   -1.8785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  3 11  1  0  0  0  0
  6 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0253071 (Heliotridine)

HMDB0257184
     RDKit          3D
RETRONECINE
 24 25  0  0  0  0  0  0  0  0999 V2000
    3.0304    0.7693    1.2476 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4178    0.9768   -0.0079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3205    0.0047   -0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2254   -0.8833   -1.2166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0499   -1.6674   -1.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5884   -1.2641    0.1831 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9777   -0.9780    0.2033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1482    0.4441    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7833    1.0719    0.5352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7059    1.6088   -0.7417 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1338   -0.1030    0.6447 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1948   -0.1942    1.3172 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2226    0.8842   -0.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0043    1.9986    0.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9474   -1.0331   -2.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2532   -2.7346   -1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7238   -1.4245   -1.9358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4530   -1.6419    0.9766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5104   -1.1580   -0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4043    0.4957    1.7678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8690    1.0219    0.1150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5835    1.8184    1.3162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4148    2.2960   -0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4622   -0.3083    1.6875 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11  3  1  0
 11  6  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
M  END
Download

3D SDF for HMDB0253071 (Heliotridine)

  Mrv1533004171501502D          

 11 12  0  0  0  0            999 V2000
    0.2076   -1.8785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  3 11  1  0  0  0  0
  6 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253071

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1=CCN2CCC(O)C12

> <INCHI_IDENTIFIER>
InChI=1S/C8H13NO2/c10-5-6-1-3-9-4-2-7(11)8(6)9/h1,7-8,10-11H,2-5H2

> <INCHI_KEY>
HJSJELVDQOXCHO-UHFFFAOYSA-N

> <FORMULA>
C8H13NO2

> <MOLECULAR_WEIGHT>
155.197

> <EXACT_MASS>
155.094628663

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.37526437734185

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-ol

> <ALOGPS_LOGP>
-0.61

> <JCHEM_LOGP>
-1.1736827656666666

> <ALOGPS_LOGS>
0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.204444736057457

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.390282972623357

> <JCHEM_PKA_STRONGEST_BASIC>
8.049502186893111

> <JCHEM_POLAR_SURFACE_AREA>
43.7

> <JCHEM_REFRACTIVITY>
42.9235

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
retronecine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0253071 (Heliotridine)

HMDB0257184
     RDKit          3D
RETRONECINE
 24 25  0  0  0  0  0  0  0  0999 V2000
    3.0304    0.7693    1.2476 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4178    0.9768   -0.0079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3205    0.0047   -0.2363 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2254   -0.8833   -1.2166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0499   -1.6674   -1.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5884   -1.2641    0.1831 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9777   -0.9780    0.2033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1482    0.4441    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7833    1.0719    0.5352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7059    1.6088   -0.7417 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1338   -0.1030    0.6447 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1948   -0.1942    1.3172 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2226    0.8842   -0.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0043    1.9986    0.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9474   -1.0331   -2.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2532   -2.7346   -1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7238   -1.4245   -1.9358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4530   -1.6419    0.9766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5104   -1.1580   -0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4043    0.4957    1.7678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8690    1.0219    0.1150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5835    1.8184    1.3162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4148    2.2960   -0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4622   -0.3083    1.6875 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11  3  1  0
 11  6  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
M  END
Download

PDB for HMDB0253071 (Heliotridine)

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  O   UNK     0       0.388  -3.507   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.894  -3.186   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.834   0.294   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.775  -3.186   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    3    6                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for HMDB0253071 (Heliotridine)

COMPND    HMDB0253071
HETATM    1  O1  UNL     1       2.449   1.269   0.913  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.561  -0.081   0.510  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.194  -0.646   0.328  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.633  -1.661   0.941  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.767  -1.882   0.438  1.00  0.00           C  
HETATM    6  N1  UNL     1      -0.835  -1.102  -0.764  1.00  0.00           N  
HETATM    7  C5  UNL     1      -2.081  -0.400  -0.934  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.834   1.037  -0.529  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.424   1.113  -0.025  1.00  0.00           C  
HETATM   10  O2  UNL     1       0.260   2.220  -0.526  1.00  0.00           O  
HETATM   11  C8  UNL     1       0.208  -0.114  -0.632  1.00  0.00           C  
HETATM   12  H1  UNL     1       2.884   1.818   0.194  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.149  -0.167  -0.433  1.00  0.00           H  
HETATM   14  H3  UNL     1       3.093  -0.583   1.361  1.00  0.00           H  
HETATM   15  H4  UNL     1       1.089  -2.288   1.719  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.827  -2.963   0.149  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.525  -1.649   1.186  1.00  0.00           H  
HETATM   18  H7  UNL     1      -2.904  -0.809  -0.305  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.425  -0.382  -1.990  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.895   1.734  -1.412  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.591   1.373   0.204  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.373   1.091   1.092  1.00  0.00           H  
HETATM   23  H12 UNL     1       0.299   2.964   0.121  1.00  0.00           H  
HETATM   24  H13 UNL     1       0.660   0.107  -1.606  1.00  0.00           H  
CONECT    1    2   12
CONECT    2    3   13   14
CONECT    3    4    4   11
CONECT    4    5   15
CONECT    5    6   16   17
CONECT    6    7   11
CONECT    7    8   18   19
CONECT    8    9   20   21
CONECT    9   10   11   22
CONECT   10   23
CONECT   11   24
END
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SMILES for HMDB0253071 (Heliotridine)

OCC1=CCN2CCC(O)C12
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INCHI for HMDB0253071 (Heliotridine)

InChI=1S/C8H13NO2/c10-5-6-1-3-9-4-2-7(11)8(6)9/h1,7-8,10-11H,2-5H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
RetronecineMeSH
Retronecine, (1S-cis)-isomerMeSH
Retronecine, monohydrochloride, (1S-cis)-isomerMeSH
Retronecine, monohydrochloride, (1S-trans)-isomerMeSH
Chemical FormulaC8H13NO2
Average Molecular Weight155.197
Monoisotopic Molecular Weight155.094628663
IUPAC Name7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-ol
Traditional Nameretronecine
CAS Registry NumberNot Available
SMILES
OCC1=CCN2CCC(O)C12
InChI Identifier
InChI=1S/C8H13NO2/c10-5-6-1-3-9-4-2-7(11)8(6)9/h1,7-8,10-11H,2-5H2
InChI KeyHJSJELVDQOXCHO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassNot Available
Sub ClassNot Available
Direct ParentAlkaloids and derivatives
Alternative Parents
Substituents
  • Alkaloid or derivatives
  • Pyrrolizine
  • N-alkylpyrrolidine
  • 1,3-aminoalcohol
  • Pyrrolidine
  • Pyrroline
  • Secondary alcohol
  • Tertiary amine
  • Tertiary aliphatic amine
  • Azacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
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 ID10180
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10626
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 ]