NP-MRD: Showing NP-Card for obscuraminol a (NP0303484)

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Record Information

Version

2.0

Created at

2022-09-10 17:51:48 UTC

Updated at

2022-09-10 17:51:48 UTC

NP-MRD ID

NP0303484

Secondary Accession Numbers

None

Natural Product Identification

Common Name

obscuraminol a

Description

1-Deoxysphinga-6Z,9Z,12Z,15Z-tetraenine, also known as obscuraminol a, belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom. Thus, 1-deoxysphinga-6Z,9Z,12Z,15Z-tetraenine is considered to be a sphingoid base. 1-Deoxysphinga-6Z,9Z,12Z,15Z-tetraenine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on 1-deoxysphinga-6Z,9Z,12Z,15Z-tetraenine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 51 50  0  0  0  0  0  0  0  0999 V2000
    8.2278    0.0111   -0.2206 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1239   -0.9339    0.2584 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4144   -0.3767    1.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1351   -0.0976    1.4865 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1921   -0.3126    0.3631 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0838   -1.2147    0.7278 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8423   -0.7990    0.7080 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5193    0.6334    0.3102 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8146    1.2319    1.4720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3533    1.7534    1.4035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2441    1.9129    0.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9964    1.5617   -1.0583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6781    0.6607   -1.7429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8281   -0.1375   -1.1782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0850    0.1223   -1.9383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2551   -0.6552   -1.4332 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0927   -2.0372   -1.4589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8733   -0.1477   -0.1572 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.1030   -0.5696    1.0666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2238   -0.7094   -0.0116 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8216    0.9899   -0.4952 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7611   -0.5001   -1.0539 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9686    0.1718    0.5949 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5412   -1.2533   -0.5965 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6769   -1.8816    0.5858 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0071   -0.1688    2.3363 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7440    0.3193    2.4299 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9766    0.5769   -0.2025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7776   -0.9523   -0.4034 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2819   -2.2661    1.0256 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0093   -1.4419    0.9681 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4159    1.2209    0.1532 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9222    0.4886   -0.5950 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3839    1.2004    2.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7210    2.1525    2.4133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4421    3.0802    0.2582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2889    1.5854    0.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1946    2.1100   -1.6057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3718    0.4953   -2.7922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5471   -1.2156   -1.4298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8962   -0.0928   -0.1090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9034   -0.0813   -3.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3873    1.1982   -1.9151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0972   -0.4735   -2.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8636   -2.5208   -1.8232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8780    0.9531   -0.1974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5131    0.2428    1.5260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8543   -0.8724    1.8577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5360   -1.4826    0.8177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8202   -0.4075   -0.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5938   -0.3365    0.8896 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  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18 20  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  2 25  1  0
  3 26  1  0
  4 27  1  0
  5 28  1  0
  5 29  1  0
  6 30  1  0
  7 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
 10 35  1  0
 11 36  1  0
 11 37  1  0
 12 38  1  0
 13 39  1  0
 14 40  1  0
 14 41  1  0
 15 42  1  0
 15 43  1  0
 16 44  1  6
 17 45  1  0
 18 46  1  6
 19 47  1  0
 19 48  1  0
 19 49  1  0
 20 50  1  0
 20 51  1  0
M  END


  Mrv1652309102219512D          

 20 19  0  0  1  0            999 V2000
    2.6664    3.1895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.6020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    4.8395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    4.8395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    4.4270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    3.6020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    3.1895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 N   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  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  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0303484

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C/C\C=C/C\C=C/C\C=C/CC[C@@H](O)[C@H](C)N

> <INCHI_IDENTIFIER>
InChI=1S/C18H31NO/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-18(20)17(2)19/h4-5,7-8,10-11,13-14,17-18,20H,3,6,9,12,15-16,19H2,1-2H3/b5-4-,8-7-,11-10-,14-13-/t17-,18+/m0/s1

> <INCHI_KEY>
YNNQTVPKSXTDCK-SABUVIKOSA-N

> <FORMULA>
C18H31NO

> <MOLECULAR_WEIGHT>
277.452

> <EXACT_MASS>
277.240564622

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
33.898159093057494

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R,6Z,9Z,12Z,15Z)-2-aminooctadeca-6,9,12,15-tetraen-3-ol

> <JCHEM_LOGP>
4.371817585333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.610296499617892

> <JCHEM_PKA_STRONGEST_BASIC>
9.832293920159957

> <JCHEM_POLAR_SURFACE_AREA>
46.25

> <JCHEM_REFRACTIVITY>
93.85210000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
obscuraminol A

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       4.977   5.954   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.644   6.724   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.644   8.264   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   9.034   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.976   8.264   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.357   9.034   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.691   8.264   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.691   6.724   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.025   5.954   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.025   4.414   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.691   3.644   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.691   2.104   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       4.977  -0.206   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

View in JSmol

Synonyms

Value	Source
Obscuraminol a	ChEBI

Chemical Formula

C₁₈H₃₁NO

Average Mass

277.4520 Da

Monoisotopic Mass

277.24056 Da

IUPAC Name

(2S,3R,6Z,9Z,12Z,15Z)-2-aminooctadeca-6,9,12,15-tetraen-3-ol

Traditional Name

obscuraminol A

CAS Registry Number

Not Available

SMILES

CC\C=C/C\C=C/C\C=C/C\C=C/CC[C@@H](O)[C@H](C)N

InChI Identifier

InChI=1S/C18H31NO/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-18(20)17(2)19/h4-5,7-8,10-11,13-14,17-18,20H,3,6,9,12,15-16,19H2,1-2H3/b5-4-,8-7-,11-10-,14-13-/t17-,18+/m0/s1

InChI Key

YNNQTVPKSXTDCK-SABUVIKOSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

1,2-aminoalcohols

Alternative Parents

Substituents

Secondary alcohol
1,2-aminoalcohol
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Organooxygen compound
Primary aliphatic amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

sphingoid (CHEBI:73892 )
amino alcohol (CHEBI:73892 )
Sphingoid base analogs (LMSP01080035 )

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	4.37	ChemAxon
pKa (Strongest Acidic)	14.61	ChemAxon
pKa (Strongest Basic)	9.83	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	46.25 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	93.85 m³·mol⁻¹	ChemAxon
Polarizability	33.9 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	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

Not Available

Chemspider ID

8237628

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10062076

PDB ID

Not Available

ChEBI ID

73892

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for obscuraminol a (NP0303484)

MOL for NP0303484 (obscuraminol a)

3D MOL for NP0303484 (obscuraminol a)

3D SDF for NP0303484 (obscuraminol a)

3D-SDF for NP0303484 (obscuraminol a)

PDB for NP0303484 (obscuraminol a)

3D PDB for NP0303484 (obscuraminol a)

SMILES for NP0303484 (obscuraminol a)

INCHI for NP0303484 (obscuraminol a)

Structure for NP0303484 (obscuraminol a)

3D Structure for NP0303484 (obscuraminol a)