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Showing NP-Card for Heliotridine (NP0051163)

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Record Information
Version1.0
Created at2022-04-27 22:34:17 UTC
Updated at2022-04-27 22:34:17 UTC
NP-MRD IDNP0051163
Secondary Accession NumbersNone
Natural Product Identification
Common NameHeliotridine
DescriptionHeliotridine, also known as retronecine, 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. Heliotridine is found in Cynoglossum zeylanicum, Heliotropium ellipticum and Heliotropium spp.. It was first documented in 2018 (PMID: 29968391). Based on a literature review a significant number of articles have been published on Heliotridine (PMID: 34069968) (PMID: 34158818) (PMID: 33379168) (PMID: 29665350).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0051163 (Heliotridine)


  Mrv1652304282200342D          

 11 12  0  0  1  0            999 V2000
    0.7846   -1.0799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0619   -2.2910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 C   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
    1.5692   -1.3349    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8242   -2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10 11  1  6  0  0  0
M  END
Download

3D MOL for NP0051163 (Heliotridine)

     RDKit          3D

 24 25  0  0  0  0  0  0  0  0999 V2000
    3.6121    0.5092   -0.0384 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3648    1.0713    0.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2777    0.1297   -0.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5328   -1.0832   -0.7260 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1937   -1.7476   -1.0179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5699   -1.1168    0.0233 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9637   -0.9836   -0.1406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2426    0.2738    0.7102 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8526    0.9182    0.9119 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9823    2.2796    0.8206 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1555    0.2652   -0.2248 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8922   -0.0917    0.7033 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2669    1.4383    1.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877    1.9387   -0.5442 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4993   -1.5530   -0.9034 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3412   -2.8118   -0.7474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1432   -1.5594   -2.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5736   -1.8045    0.2818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2070   -0.7932   -1.1998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8637    0.9665    0.1042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7073    0.0183    1.6612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4971    0.5651    1.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9029    2.5789    0.5366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6068    0.5919   -1.1865 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  1
 10 23  1  0
 11 24  1  6
M  END
Download

3D SDF for NP0051163 (Heliotridine)


  Mrv1652304282200342D          

 11 12  0  0  1  0            999 V2000
    0.7846   -1.0799    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0619   -2.2910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 C   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
    1.5692   -1.3349    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8242   -2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10 11  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051163

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=CCN2CC[C@H](O)[C@@H]12

> <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/t7-,8+/m0/s1

> <INCHI_KEY>
HJSJELVDQOXCHO-JGVFFNPUSA-N

> <FORMULA>
C8H13NO2

> <MOLECULAR_WEIGHT>
155.197

> <EXACT_MASS>
155.094628663

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.491094873659087

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,7aR)-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>
heliotridine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0051163 (Heliotridine)

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PDB for NP0051163 (Heliotridine)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.465  -2.016   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.465  -0.476   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.905  -1.246   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.000  -2.492   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.476  -3.956   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.982  -4.277   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.929   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.929  -2.492   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.405  -3.956   0.000  0.00  0.00           O+0
CONECT    1    2    5   10                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    2    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    1   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

Download
3D PDB for NP0051163 (Heliotridine)
Download
SMILES for NP0051163 (Heliotridine)
OCC1=CCN2CC[C@H](O)[C@@H]12
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INCHI for NP0051163 (Heliotridine)
InChI=1S/C8H13NO2/c10-5-6-1-3-9-4-2-7(11)8(6)9/h1,7-8,10-11H,2-5H2/t7-,8+/m0/s1
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View in JSmol
Synonyms
ValueSource
RetronecineMeSH
Retronecine, (1S-cis)-isomerMeSH
Retronecine, monohydrochloride, (1S-cis)-isomerMeSH
Retronecine, monohydrochloride, (1S-trans)-isomerMeSH
Chemical FormulaC8H13NO2
Average Mass155.1970 Da
Monoisotopic Mass155.09463 Da
IUPAC Name(1S,7aR)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-ol
Traditional Nameheliotridine
CAS Registry NumberNot Available
SMILES
OCC1=CCN2CC[C@H](O)[C@@H]12
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/t7-,8+/m0/s1
InChI KeyHJSJELVDQOXCHO-JGVFFNPUSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cynoglossum zeylanicumLOTUS Database
Heliotropium ellipticumLOTUS Database
Heliotropium spp.Plant
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 Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.61ALOGPS
logP-1.2ChemAxon
logS0.62ALOGPS
pKa (Strongest Acidic)14.39ChemAxon
pKa (Strongest Basic)8.05ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area43.7 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity42.92 m³·mol⁻¹ChemAxon
Polarizability16.49 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00002089  
Chemspider ID391082  
KEGG Compound IDC10321  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound442736  
PDB IDNot Available
ChEBI ID5642  
Good Scents IDNot Available
References
General References
  1. Gluck J, Henricsson M, Braeuning A, Hessel-Pras S: The Food Contaminants Pyrrolizidine Alkaloids Disturb Bile Acid Homeostasis Structure-Dependently in the Human Hepatoma Cell Line HepaRG. Foods. 2021 May 18;10(5). pii: foods10051114. doi: 10.3390/foods10051114. [PubMed:34069968  ] 
  2. Sarkar C, Mondal M, Khanom B, Hossain MM, Hossain MS, Sureda A, Islam MT, Martorell M, Kumar M, Sharifi-Rad J, Al-Harrasi A, Al-Rawahi A: Heliotropium indicum L.: From Farm to a Source of Bioactive Compounds with Therapeutic Activity. Evid Based Complement Alternat Med. 2021 Jun 1;2021:9965481. doi: 10.1155/2021/9965481. eCollection 2021. [PubMed:34158818  ] 
  3. Gluck J, Waizenegger J, Braeuning A, Hessel-Pras S: Pyrrolizidine Alkaloids Induce Cell Death in Human HepaRG Cells in a Structure-Dependent Manner. Int J Mol Sci. 2020 Dec 28;22(1). pii: ijms22010202. doi: 10.3390/ijms22010202. [PubMed:33379168  ] 
  4. Colegate SM, Upton R, Gardner DR, Panter KE, Betz JM: Potentially toxic pyrrolizidine alkaloids in Eupatorium perfoliatum and three related species. Implications for herbal use as boneset. Phytochem Anal. 2018 Nov;29(6):613-626. doi: 10.1002/pca.2775. Epub 2018 Jul 2. [PubMed:29968391  ] 
  5. Luckert C, Braeuning A, Lampen A, Hessel-Pras S: PXR: Structure-specific activation by hepatotoxic pyrrolizidine alkaloids. Chem Biol Interact. 2018 May 25;288:38-48. doi: 10.1016/j.cbi.2018.04.017. Epub 2018 Apr 14. [PubMed:29665350  ]