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Showing metabocard for Supinidine (HMDB0302361)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:12:08 UTC
Update Date2021-09-23 17:12:08 UTC
HMDB IDHMDB0302361
Secondary Accession NumbersNone
Metabolite Identification
Common NameSupinidine
Description[(7aS)-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methanol 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 [(7aS)-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methanol.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302361 (Supinidine)

  Mrv1533007131513352D          

 11 12  0  0  1  0            999 V2000
    0.7846    1.0799    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
    3.3237    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -0.3721    0.0000 C   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
    2.0542    0.6674    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0542    1.4924    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9007   -0.5436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.1576    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  7  3  2  0  0  0  0
  7  6  1  0  0  0  0
  8  2  1  0  0  0  0
  8  7  1  0  0  0  0
  9  4  1  0  0  0  0
  9  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  1  0  0  0  0
  8 11  1  1  0  0  0
M  END
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3D MOL for HMDB0302361 (Supinidine)

HMDB0302361
     RDKit          3D
Supinidine
 23 24  0  0  0  0  0  0  0  0999 V2000
    2.9882   -1.1066    0.7058 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4359   -0.6307   -0.4920 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2413    0.1982   -0.2080 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1235    1.4755   -0.5499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2079    1.9703   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8315    0.8677    0.5560 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1128    0.5129    0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9634   -0.7501   -0.7656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6814   -1.3587   -0.2636 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0305   -0.2636    0.4826 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3292   -1.6523    1.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2238   -0.0575   -1.0345 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1563   -1.5113   -1.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8680    2.0774   -1.0728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7795    2.3277   -0.9747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0220    2.7717    0.6526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7970    0.3131    0.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5804    1.3269   -0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8203   -1.4554   -0.5930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9182   -0.5447   -1.8472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0571   -1.7353   -1.1020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9010   -2.1866    0.4344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2756   -0.5887    1.5274 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
 10  3  1  0
 10  6  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
  9 21  1  0
  9 22  1  0
 10 23  1  1
M  END
Download

3D SDF for HMDB0302361 (Supinidine)

  Mrv1533007131513352D          

 11 12  0  0  1  0            999 V2000
    0.7846    1.0799    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
    3.3237    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -0.3721    0.0000 C   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
    2.0542    0.6674    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0542    1.4924    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9007   -0.5436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.1576    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  7  3  2  0  0  0  0
  7  6  1  0  0  0  0
  8  2  1  0  0  0  0
  8  7  1  0  0  0  0
  9  4  1  0  0  0  0
  9  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  1  0  0  0  0
  8 11  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0302361

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@]12CCCN1CC=C2CO

> <INCHI_IDENTIFIER>
InChI=1S/C8H13NO/c10-6-7-3-5-9-4-1-2-8(7)9/h3,8,10H,1-2,4-6H2/t8-/m0/s1

> <INCHI_KEY>
XMJAZPFSQQKHEG-QMMMGPOBSA-N

> <FORMULA>
C8H13NO

> <MOLECULAR_WEIGHT>
139.198

> <EXACT_MASS>
139.099714043

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.655300199732139

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(7aS)-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methanol

> <ALOGPS_LOGP>
0.44

> <JCHEM_LOGP>
-0.02598515266666683

> <ALOGPS_LOGS>
0.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.110551118005858

> <JCHEM_PKA_STRONGEST_BASIC>
9.692866022495073

> <JCHEM_POLAR_SURFACE_AREA>
23.47

> <JCHEM_REFRACTIVITY>
41.6056

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.62e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
supinidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302361 (Supinidine)

HMDB0302361
     RDKit          3D
Supinidine
 23 24  0  0  0  0  0  0  0  0999 V2000
    2.9882   -1.1066    0.7058 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4359   -0.6307   -0.4920 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2413    0.1982   -0.2080 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1235    1.4755   -0.5499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2079    1.9703   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8315    0.8677    0.5560 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1128    0.5129    0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9634   -0.7501   -0.7656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6814   -1.3587   -0.2636 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0305   -0.2636    0.4826 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3292   -1.6523    1.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2238   -0.0575   -1.0345 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1563   -1.5113   -1.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8680    2.0774   -1.0728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7795    2.3277   -0.9747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0220    2.7717    0.6526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7970    0.3131    0.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5804    1.3269   -0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8203   -1.4554   -0.5930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9182   -0.5447   -1.8472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0571   -1.7353   -1.1020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9010   -2.1866    0.4344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2756   -0.5887    1.5274 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
 10  3  1  0
 10  6  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
  9 21  1  0
  9 22  1  0
 10 23  1  1
M  END
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PDB for HMDB0302361 (Supinidine)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       1.465   2.016   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.204   2.016   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.370   3.262   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.299   3.262   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.775  -0.695   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.834   1.246   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.834   2.786   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       7.281  -1.015   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       3.834  -0.294   0.000  0.00  0.00           H+0
CONECT    1    2    4                                                       
CONECT    2    1    8                                                       
CONECT    3    5    7                                                       
CONECT    4    1    9                                                       
CONECT    5    3    9                                                       
CONECT    6    7   10                                                       
CONECT    7    3    6    8                                                  
CONECT    8    2    7    9   11                                             
CONECT    9    4    5    8                                                  
CONECT   10    6                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for HMDB0302361 (Supinidine)

COMPND    HMDB0302361
HETATM    1  O1  UNL     1       2.988  -1.107   0.706  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.436  -0.631  -0.492  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.241   0.198  -0.208  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.124   1.476  -0.550  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.208   1.970  -0.101  1.00  0.00           C  
HETATM    6  N1  UNL     1      -0.831   0.868   0.556  1.00  0.00           N  
HETATM    7  C5  UNL     1      -2.113   0.513   0.015  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.963  -0.750  -0.766  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.681  -1.359  -0.264  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.031  -0.264   0.483  1.00  0.00           C  
HETATM   11  H1  UNL     1       2.329  -1.652   1.185  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.224  -0.058  -1.035  1.00  0.00           H  
HETATM   13  H3  UNL     1       2.156  -1.511  -1.119  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.868   2.077  -1.073  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.779   2.328  -0.975  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.022   2.772   0.653  1.00  0.00           H  
HETATM   17  H7  UNL     1      -2.797   0.313   0.866  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.580   1.327  -0.575  1.00  0.00           H  
HETATM   19  H9  UNL     1      -2.820  -1.455  -0.593  1.00  0.00           H  
HETATM   20  H10 UNL     1      -1.918  -0.545  -1.847  1.00  0.00           H  
HETATM   21  H11 UNL     1      -0.057  -1.735  -1.102  1.00  0.00           H  
HETATM   22  H12 UNL     1      -0.901  -2.187   0.434  1.00  0.00           H  
HETATM   23  H13 UNL     1       0.276  -0.589   1.527  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    4   10
CONECT    4    5   14
CONECT    5    6   15   16
CONECT    6    7   10
CONECT    7    8   17   18
CONECT    8    9   19   20
CONECT    9   10   21   22
CONECT   10   23
END
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SMILES for HMDB0302361 (Supinidine)

[H][C@@]12CCCN1CC=C2CO
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INCHI for HMDB0302361 (Supinidine)

InChI=1S/C8H13NO/c10-6-7-3-5-9-4-1-2-8(7)9/h3,8,10H,1-2,4-6H2/t8-/m0/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H13NO
Average Molecular Weight139.198
Monoisotopic Molecular Weight139.099714043
IUPAC Name[(7aS)-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methanol
Traditional Namesupinidine
CAS Registry NumberNot Available
SMILES
[H][C@@]12CCCN1CC=C2CO
InChI Identifier
InChI=1S/C8H13NO/c10-6-7-3-5-9-4-1-2-8(7)9/h3,8,10H,1-2,4-6H2/t8-/m0/s1
InChI KeyXMJAZPFSQQKHEG-QMMMGPOBSA-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
  • Tertiary amine
  • Tertiary aliphatic amine
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Organic nitrogen compound
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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 LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB004294
KNApSAcK IDC00002120
Chemspider ID144350
KEGG Compound IDC10400
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound164663
PDB IDNot Available
ChEBI ID9360
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 ReferencesNot Available