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Showing NP-Card for Trachelanthamidine (NP0140059)

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Record Information
Version2.0
Created at2022-06-29 20:44:11 UTC
Updated at2022-06-29 20:44:11 UTC
NP-MRD IDNP0140059
Secondary Accession NumbersNone
Natural Product Identification
Common NameTrachelanthamidine
DescriptionTrachelanthamidine belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom. Trachelanthamidine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Trachelanthamidine is found in Pulmonaria obscura and Trachelanthus korolkowii. Trachelanthamidine was first documented in 2011 (PMID: 21500327). Based on a literature review a small amount of articles have been published on Trachelanthamidine (PMID: 32459490) (PMID: 34447481) (PMID: 27409574) (PMID: 25264221).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0140059 (Trachelanthamidine)


  Mrv1652306292222442D          

 10 11  0  0  1  0            999 V2000
    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 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  1  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
    2.0542   -0.6674    0.0000 N   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
    3.0937    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5417    1.8102    0.0000 O   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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  1  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
  4  9  1  6  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0140059 (Trachelanthamidine)

     RDKit          3D

 25 26  0  0  0  0  0  0  0  0999 V2000
    2.8593   -0.8413    0.3814 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3072   -0.3794   -0.7808 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9685    0.2892   -0.5885 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1610    1.4838    0.3555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2509    1.6658    0.8675 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7447    0.3343    1.0291 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1270    0.2944    0.6291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2922   -1.1027    0.0655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9904   -1.2461   -0.7283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0063   -0.5414    0.1706 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1098   -1.8104    0.2555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1502   -1.2123   -1.5114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0184    0.3206   -1.2616 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5226    0.6176   -1.5346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5061    2.3316   -0.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8260    1.1785    1.1793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8362    2.2028    0.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2375    2.2631    1.8006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8023    0.4901    1.4680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2718    1.0206   -0.2167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1722   -1.1801   -0.5794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3378   -1.8220    0.8903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0949   -0.7134   -1.6817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7472   -2.3146   -0.8564 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4821   -1.3285    0.7877 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  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
  3 14  1  6
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  1
M  END
Download

3D SDF for NP0140059 (Trachelanthamidine)


  Mrv1652306292222442D          

 10 11  0  0  1  0            999 V2000
    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 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  1  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
    2.0542   -0.6674    0.0000 N   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
    3.0937    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5417    1.8102    0.0000 O   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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  1  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
  4  9  1  6  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0140059

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1CCN2CCC[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C8H15NO/c10-6-7-3-5-9-4-1-2-8(7)9/h7-8,10H,1-6H2/t7-,8-/m0/s1

> <INCHI_KEY>
LOFDEIYZIAVXHE-YUMQZZPRSA-N

> <FORMULA>
C8H15NO

> <MOLECULAR_WEIGHT>
141.214

> <EXACT_MASS>
141.115364107

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.279210851198687

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,7aS)-hexahydro-1H-pyrrolizin-1-yl]methanol

> <ALOGPS_LOGP>
0.70

> <JCHEM_LOGP>
0.03138240566666668

> <ALOGPS_LOGS>
0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.420323971873753

> <JCHEM_PKA_STRONGEST_BASIC>
10.4996142806747

> <JCHEM_POLAR_SURFACE_AREA>
23.47

> <JCHEM_REFRACTIVITY>
41.0418

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.54e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
trachelanthamidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0140059 (Trachelanthamidine)

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PDB for NP0140059 (Trachelanthamidine)
HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0       1.465  -0.476   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       3.834   0.294   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       3.834  -1.246   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.775   2.235   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.744   3.379   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    1                                                       
CONECT    9    4   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END

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3D PDB for NP0140059 (Trachelanthamidine)
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SMILES for NP0140059 (Trachelanthamidine)
OC[C@@H]1CCN2CCC[C@@H]12
Download
INCHI for NP0140059 (Trachelanthamidine)
InChI=1S/C8H15NO/c10-6-7-3-5-9-4-1-2-8(7)9/h7-8,10H,1-6H2/t7-,8-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC8H15NO
Average Mass141.2140 Da
Monoisotopic Mass141.11536 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
OC[C@@H]1CCN2CCC[C@@H]12
InChI Identifier
InChI=1S/C8H15NO/c10-6-7-3-5-9-4-1-2-8(7)9/h7-8,10H,1-6H2/t7-,8-/m0/s1
InChI KeyLOFDEIYZIAVXHE-YUMQZZPRSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Pulmonaria obscuraLOTUS Database
Trachelanthus korolkowiiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrrolizidines  
Sub ClassNot Available
Direct ParentPyrrolizidines  
Alternative Parents
Substituents
  • Pyrrolizidine
    • 

  • N-alkylpyrrolidine
    • 

  • 1,3-aminoalcohol
    • 

  • Pyrrolidine
    • 

  • Tertiary amine
    • 

  • Tertiary aliphatic amine
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Organic nitrogen compound
    • 

  • 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
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID163655  
KEGG Compound IDC12440  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound188288  
PDB IDNot Available
ChEBI ID32249  
Good Scents IDNot Available
References
General References
  1. Sarkale AM, Appayee C: Stereodivergent Synthesis of 1-Hydroxymethylpyrrolizidine Alkaloids. Org Lett. 2020 Jun 5;22(11):4355-4359. doi: 10.1021/acs.orglett.0c01375. Epub  2020 May 27. [PubMed:32459490  ] 
  2. Blank BR, Andrews IP, Kwon O: Phosphine-Catalyzed (4+1) Annulation: Rearrangement of Allenylic Carbamates to 3-Pyrrolines through Phosphonium Diene Intermediates. ChemCatChem. 2020 Sep 4;12(17):4352-4372. doi: 10.1002/cctc.202000626. Epub 2020  May 22. [PubMed:34447481  ] 
  3. Moragas T, Liffey RM, Regentova D, Ward JP, Dutton J, Lewis W, Churcher I, Walton L, Souto JA, Stockman RA: Sigmatropic Rearrangement of Vinyl Aziridines: Expedient Synthesis of Cyclic Sulfoximines from Chiral Sulfinimines. Angew Chem Int Ed Engl. 2016 Aug 16;55(34):10047-51. doi: 10.1002/anie.201604188.  Epub 2016 Jul 13. [PubMed:27409574  ] 
  4. Koley D, Krishna Y, Srinivas K, Khan AA, Kant R: Organocatalytic asymmetric Mannich cyclization of hydroxylactams with acetals: total syntheses of (-)-epilupinine, (-)-tashiromine, and (-)-trachelanthamidine. Angew Chem Int Ed Engl. 2014 Nov 24;53(48):13196-200. doi:  10.1002/anie.201407185. Epub 2014 Sep 26. [PubMed:25264221  ] 
  5. Nicolai S, Piemontesi C, Waser J: A palladium-catalyzed aminoalkynylation strategy towards bicyclic heterocycles: synthesis of (+/-)-trachelanthamidine. Angew Chem Int Ed Engl. 2011 May 9;50(20):4680-3. doi: 10.1002/anie.201100718.  Epub 2011 Apr 15. [PubMed:21500327  ]