NP-MRD: Showing NP-Card for (-)-Sedamine (NP0051149)

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Record Information

Version

2.0

Created at

2022-04-27 22:33:43 UTC

Updated at

2022-04-27 22:33:43 UTC

NP-MRD ID

NP0051149

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Sedamine

Description

(-)-Sedamine belongs to the class of organic compounds known as aralkylamines. These are alkylamines in which the alkyl group is substituted at one carbon atom by an aromatic hydrocarbyl group (-)-Sedamine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. (-)-Sedamine is found in Phedimus hybridus, Sedum acre , Phedimus aizoon and Sedum lydium. (-)-Sedamine was first documented in 2011 (PMID: 21506188). Based on a literature review very few articles have been published on (-)-Sedamine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    1.5602    2.2157   -1.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0788    1.0197   -0.5952 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712    1.1309    0.3956 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8016   -0.1030    0.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3568   -1.2842   -0.0847 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8281   -1.3094    0.0531 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2682   -0.1296   -0.6450 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1440    0.2143   -0.1798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0473   -0.9994   -0.2193 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0953   -1.4609   -1.5376 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4151   -0.5252    0.1345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0133   -0.8471    1.3399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2591   -0.4229    1.6774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9667    0.3568    0.7994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4081    0.7003   -0.4116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1491    0.2639   -0.7372 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0772    2.0510   -2.0751 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3666    2.9740   -1.1847 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8276    2.6431   -0.3503 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6052    1.6026    1.3105 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8183    1.8893    0.0498 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5814   -0.3676    1.8092 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9031    0.0073    0.6810 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6722   -1.2053   -1.1235 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7365   -2.1964    0.4049 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6426   -1.3402    1.1420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4366   -2.2432   -0.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1536   -0.4122   -1.7309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1420    0.6349    0.8386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6093    0.9705   -0.8454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7759   -1.7755    0.4903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9352   -2.4491   -1.5933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4638   -1.4679    2.0523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7197   -0.6790    2.6222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9674    0.7069    1.0520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9826    1.3187   -1.0954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6917    0.5185   -1.6760 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
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
  7  2  1  0
 16 11  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  6
  8 29  1  0
  8 30  1  0
  9 31  1  1
 10 32  1  0
 12 33  1  0
 13 34  1  0
 14 35  1  0
 15 36  1  0
 16 37  1  0
M  END


  Mrv1652304282200332D          

 16 17  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
  8 15  1  6  0  0  0
  3 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051149

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CCCC[C@H]1C[C@H](O)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H21NO/c1-15-10-6-5-9-13(15)11-14(16)12-7-3-2-4-8-12/h2-4,7-8,13-14,16H,5-6,9-11H2,1H3/t13-,14-/m0/s1

> <INCHI_KEY>
GOWRYACIDZSIHI-KBPBESRZSA-N

> <FORMULA>
C14H21NO

> <MOLECULAR_WEIGHT>
219.328

> <EXACT_MASS>
219.1623143

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.53092936795138

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S)-2-[(2S)-1-methylpiperidin-2-yl]-1-phenylethan-1-ol

> <ALOGPS_LOGP>
2.62

> <JCHEM_LOGP>
2.254400581666667

> <ALOGPS_LOGS>
-1.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.434260987573115

> <JCHEM_PKA_STRONGEST_BASIC>
9.245964351169265

> <JCHEM_POLAR_SURFACE_AREA>
23.47

> <JCHEM_REFRACTIVITY>
67.24080000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.14e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-sedamine

> <JCHEM_VEBER_RULE>
1

$$$$

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       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.334  -5.390   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   16                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9                                                       
CONECT   15    8                                                            
CONECT   16    3                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₂₁NO

Average Mass

219.3280 Da

Monoisotopic Mass

219.16231 Da

IUPAC Name

(1S)-2-[(2S)-1-methylpiperidin-2-yl]-1-phenylethan-1-ol

Traditional Name

(-)-sedamine

CAS Registry Number

Not Available

SMILES

CN1CCCC[C@H]1C[C@H](O)C1=CC=CC=C1

InChI Identifier

InChI=1S/C14H21NO/c1-15-10-6-5-9-13(15)11-14(16)12-7-3-2-4-8-12/h2-4,7-8,13-14,16H,5-6,9-11H2,1H3/t13-,14-/m0/s1

InChI Key

GOWRYACIDZSIHI-KBPBESRZSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Phedimus hybridus	LOTUS Database	35616633
Sedum acre	Plant	KNApSAcK
Sedum aizoon	LOTUS Database	35616633
Sedum lydium	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aralkylamines. These are alkylamines in which the alkyl group is substituted at one carbon atom by an aromatic hydrocarbyl group.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

Aralkylamines

Alternative Parents

Substituents

Aralkylamine
Monocyclic benzene moiety
Piperidine
Benzenoid
1,3-aminoalcohol
Secondary alcohol
Tertiary amine
Tertiary aliphatic amine
Azacycle
Organoheterocyclic compound
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organopnictogen compound
Aromatic alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

citraconoyl group (CHEBI:116 )
Piperidine alkaloids (C10171 )

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	2.62	ALOGPS
logP	2.25	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	14.43	ChemAxon
pKa (Strongest Basic)	9.25	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	23.47 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	67.24 m³·mol⁻¹	ChemAxon
Polarizability	25.53 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002072

Chemspider ID

391018

KEGG Compound ID

C10171

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442657

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Riva E, Rencurosi A, Gagliardi S, Passarella D, Martinelli M: Synthesis of (+)-dumetorine and congeners by using flow chemistry technologies. Chemistry. 2011 May 23;17(22):6221-6. doi: 10.1002/chem.201100300. Epub 2011 Apr 19. [PubMed:21506188 ]

Showing NP-Card for (-)-Sedamine (NP0051149)

MOL for NP0051149 ((-)-Sedamine)

3D MOL for NP0051149 ((-)-Sedamine)

3D SDF for NP0051149 ((-)-Sedamine)

3D-SDF for NP0051149 ((-)-Sedamine)

PDB for NP0051149 ((-)-Sedamine)

3D PDB for NP0051149 ((-)-Sedamine)

SMILES for NP0051149 ((-)-Sedamine)

INCHI for NP0051149 ((-)-Sedamine)

Structure for NP0051149 ((-)-Sedamine)

3D Structure for NP0051149 ((-)-Sedamine)