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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2022-09-09 19:39:11 UTC

Update Date

2022-09-22 18:35:06 UTC

HMDB ID

HMDB0341200

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Trachelanthine

Description

Trachelanthine 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. Based on a literature review very few articles have been published on Trachelanthine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309092222172D          

 24 25  0  0  1  0            999 V2000
   -2.4682   -3.1777    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6612   -3.0062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9162   -3.7908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2133   -2.3931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8543   -2.8347    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6827   -3.6416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0258   -2.0277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4127   -1.4757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8104   -1.7728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0473   -2.6631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5047   -3.2762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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  1  0  0  0  0  0  0  0  0  0
    1.8529   -1.5057    0.0000 H   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
    2.0542    0.9826    0.0000 O   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
    2.0542   -0.6674    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3867   -0.1825    0.0000 H   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
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  5 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  1  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 14 23  1  0  0  0  0
 18 23  1  0  0  0  0
 23 24  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0341200

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]C(C)(O)[C@](O)(C(C)C)C(=O)OC[C@@]1([H])CCN2(=O)CCC[C@@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C15H27NO5/c1-10(2)15(19,11(3)17)14(18)21-9-12-6-8-16(20)7-4-5-13(12)16/h10-13,17,19H,4-9H2,1-3H3/t11?,12-,13+,15-,16?/m1/s1

> <INCHI_KEY>
DLNWZIVYKQXLTN-CGYUPCHJSA-N

> <FORMULA>
C15H27NO5

> <MOLECULAR_WEIGHT>
301.383

> <EXACT_MASS>
301.188922973

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
32.50580985409503

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[(1S,7aS)-4-oxo-hexahydro-1H-4lambda5-pyrrolizin-1-yl]methyl (2R)-2,3-dihydroxy-2-(propan-2-yl)butanoate

> <JCHEM_LOGP>
-0.2104250056666679

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.80091875820806

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.34398286163501

> <JCHEM_PKA_STRONGEST_BASIC>
2.5089814005330107

> <JCHEM_POLAR_SURFACE_AREA>
93.64000000000001

> <JCHEM_REFRACTIVITY>
78.10570000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,7aS)-4-oxo-hexahydro-1H-4lambda5-pyrrolizin-1-yl]methyl (2R)-2,3-dihydroxy-2-isopropylbutanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  H   UNK     0      -4.607  -5.932   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -3.101  -5.612   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.577  -7.076   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -4.131  -4.467   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.595  -5.291   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.274  -6.798   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.915  -3.785   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.770  -2.755   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.379  -3.309   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.088  -4.971   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.942  -6.116   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.388  -3.507   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.894  -3.186   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       3.459  -2.811   0.000  0.00  0.00           H+0
HETATM   16  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       3.834   0.294   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0       3.834   1.834   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM   24  H   UNK     0       2.589  -0.341   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6    7   10                                             
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   23                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20   23                                             
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   14   18   24                                             
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₅H₂₇NO₅

Average Molecular Weight

301.383

Monoisotopic Molecular Weight

301.188922973

IUPAC Name

[(1S,7aS)-4-oxo-hexahydro-1H-4lambda5-pyrrolizin-1-yl]methyl (2R)-2,3-dihydroxy-2-(propan-2-yl)butanoate

Traditional Name

[(1S,7aS)-4-oxo-hexahydro-1H-4lambda5-pyrrolizin-1-yl]methyl (2R)-2,3-dihydroxy-2-isopropylbutanoate

CAS Registry Number

Not Available

SMILES

[H]C(C)(O)[C@](O)(C(C)C)C(=O)OC[C@@]1([H])CCN2(=O)CCC[C@@]12[H]

InChI Identifier

InChI=1S/C15H27NO5/c1-10(2)15(19,11(3)17)14(18)21-9-12-6-8-16(20)7-4-5-13(12)16/h10-13,17,19H,4-9H2,1-3H3/t11?,12-,13+,15-,16?/m1/s1

InChI Key

DLNWZIVYKQXLTN-CGYUPCHJSA-N

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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolizidines

Sub Class

Not Available

Direct Parent

Pyrrolizidines

Alternative Parents

Substituents

Pyrrolizidine
Beta-hydroxy acid
Fatty acid ester
Hydroxy acid
Fatty acyl
N-alkylpyrrolidine
Pyrrolidine
Trialkyl amine oxide
Tertiary alcohol
1,2-diol
Carboxylic acid ester
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
N-oxide
Azacycle
Trisubstituted n-oxide
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Organic zwitterion
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-0.21	ChemAxon
pKa (Strongest Acidic)	11.34	ChemAxon
pKa (Strongest Basic)	2.51	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.64 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	78.11 m³·mol⁻¹	ChemAxon
Polarizability	32.51 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

10086

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10523

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864 ]

Showing metabocard for Trachelanthine (HMDB0341200)

MOL for HMDB0341200 (Trachelanthine)

3D MOL for HMDB0341200 (Trachelanthine)

3D SDF for HMDB0341200 (Trachelanthine)

3D-SDF for HMDB0341200 (Trachelanthine)

PDB for HMDB0341200 (Trachelanthine)

3D PDB for HMDB0341200 (Trachelanthine)

SMILES for HMDB0341200 (Trachelanthine)

INCHI for HMDB0341200 (Trachelanthine)

Structure for HMDB0341200 (Trachelanthine)

3D Structure for HMDB0341200 (Trachelanthine)

Predicted Kovats Retention Indices