NP-MRD: Showing NP-Card for (2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol (NP0229377)

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Record Information

Version

2.0

Created at

2022-09-06 09:24:22 UTC

Updated at

2022-09-06 09:24:22 UTC

NP-MRD ID

NP0229377

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol

Description

Raspailyne b2 belongs to the class of organic compounds known as glycerol vinyl ethers. These are lipids containing a vinyl ether derivative of glycerol. Thus, raspailyne B2 is considered to be a monoradylglycerol. (2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol is found in Raspailia ramosa. Based on a literature review very few articles have been published on Raspailyne b2.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 45 44  0  0  0  0  0  0  0  0999 V2000
    7.5996   -0.9062   -1.3260 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0857   -1.0574   -1.1447 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5806    0.2245   -0.5455 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0411    0.0607   -0.3653 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5660    1.3177    0.2190 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1671    1.5833    0.5048 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3547    0.7971    1.4296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1522   -0.6109    1.0861 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0709   -1.1313    0.8597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1941   -0.2495    0.9664 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1369    0.5019    1.0758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2511    1.3983    1.2291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2450    1.4414    0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1431    0.5644   -0.7305 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8735   -0.6439   -0.6287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3447   -0.3240   -0.4838 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.7364    0.3892   -1.6154 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1549   -1.5880   -0.2916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4933   -1.1940   -0.1550 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0924   -1.8953   -1.3569 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9701   -0.2598   -0.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7296   -0.3386   -2.2717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8573   -1.9037   -0.4909 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6322   -1.2607   -2.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9801    0.3543    0.4798 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7274    1.0979   -1.1781 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9652   -0.8602    0.2204 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6336   -0.1401   -1.3753 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9079    2.1464   -0.4955 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1984    1.5836    1.1391 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1030    2.6922    0.8059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5698    1.6238   -0.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3090    1.2574    1.4135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6331    0.9290    2.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9401   -1.3255    1.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2116   -2.1679    0.6075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2983    2.0649    2.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0914    2.1131    0.4546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7491   -1.1618   -1.6117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4968   -1.3160    0.1435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5466    0.3259    0.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2560    1.2379   -1.6094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8030   -2.0462    0.6549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0095   -2.2516   -1.1685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6897   -1.0725    0.8189 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  2  0
  9 10  1  0
 10 11  3  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
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  7 34  1  0
  8 35  1  0
  9 36  1  0
 12 37  1  0
 13 38  1  0
 15 39  1  0
 15 40  1  0
 16 41  1  1
 17 42  1  0
 18 43  1  0
 18 44  1  0
 19 45  1  0
M  END

  Mrv1652309062211242D          

 19 18  0  0  1  0            999 V2000
    1.0461    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -1.0461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763   -1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908   -1.0461    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052   -1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6197   -1.0461    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.6197   -0.2211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.3342   -1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0487   -1.0461    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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  3  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
M  END
> <DATABASE_ID>
NP0229377

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCC\C=C/C#C\C=C/OC[C@@H](O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C16H26O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-19-15-16(18)14-17/h8-9,12-13,16-18H,2-7,14-15H2,1H3/b9-8-,13-12-/t16-/m0/s1

> <INCHI_KEY>
GTUVAFBOEGIOIW-BJQMMIFBSA-N

> <FORMULA>
C16H26O3

> <MOLECULAR_WEIGHT>
266.381

> <EXACT_MASS>
266.188194697

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
32.03575696323169

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-3-[(1Z,5Z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol

> <JCHEM_LOGP>
3.363893533666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.562613983555693

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.625627503490044

> <JCHEM_PKA_STRONGEST_BASIC>
-2.968598186771108

> <JCHEM_POLAR_SURFACE_AREA>
49.69

> <JCHEM_REFRACTIVITY>
81.12100000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-[(1Z,5Z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       1.953   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.622   2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.622   1.127   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.622  -0.413   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.622  -1.953   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.956  -2.723   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      15.289  -1.953   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      16.623  -2.723   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      17.957  -1.953   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      17.957  -0.413   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      19.290  -2.723   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      20.624  -1.953   0.000  0.00  0.00           O+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                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₂₆O₃

Average Mass

266.3810 Da

Monoisotopic Mass

266.18819 Da

IUPAC Name

(2S)-3-[(1Z,5Z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol

Traditional Name

(2S)-3-[(1Z,5Z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol

CAS Registry Number

Not Available

SMILES

CCCCCCC\C=C/C#C\C=C/OC[C@@H](O)CO

InChI Identifier

InChI=1S/C16H26O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-19-15-16(18)14-17/h8-9,12-13,16-18H,2-7,14-15H2,1H3/b9-8-,13-12-/t16-/m0/s1

InChI Key

GTUVAFBOEGIOIW-BJQMMIFBSA-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

Species Name	Source	Reference
Raspailia ramosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerol vinyl ethers. These are lipids containing a vinyl ether derivative of glycerol.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerolipids

Sub Class

Glycerol vinyl ethers

Direct Parent

Glycerol vinyl ethers

Alternative Parents

Substituents

Glycerol vinyl ether
Monoradylglycerol
Secondary alcohol
1,2-diol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	3.36	ChemAxon
pKa (Strongest Acidic)	13.63	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	49.69 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	81.12 m³·mol⁻¹	ChemAxon
Polarizability	32.04 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

10211820

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21591333

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol (NP0229377)

MOL for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

3D MOL for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

3D SDF for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

3D-SDF for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

PDB for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

3D PDB for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

SMILES for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

INCHI for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

Structure for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)

3D Structure for NP0229377 ((2s)-3-[(1z,5z)-trideca-1,5-dien-3-yn-1-yloxy]propane-1,2-diol)