NP-MRD: Showing NP-Card for (1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol (NP0196656)

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Record Information

Version

2.0

Created at

2022-09-04 14:46:55 UTC

Updated at

2022-09-04 14:46:55 UTC

NP-MRD ID

NP0196656

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol

Description

(1'S,2S,2'R,4'S,6S,7'S,8'R,9'S,12'S,13'R,16'S)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosan]-18'-ene-6,16'-diol belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid. (1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol is found in Tacca leontopetaloides. Based on a literature review very few articles have been published on (1'S,2S,2'R,4'S,6S,7'S,8'R,9'S,12'S,13'R,16'S)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosan]-18'-ene-6,16'-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042216462D          

 32 37  0  0  1  0            999 V2000
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 24 32  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309042216462D          

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 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
  7 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  6 21  1  0  0  0  0
  3 21  1  0  0  0  0
 21 22  1  1  0  0  0
  4 23  1  1  0  0  0
 24 23  1  1  0  0  0
  2 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  1  0  0  0
 30 31  1  0  0  0  0
 28 32  1  0  0  0  0
 24 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0196656

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](C[C@@H]3[C@@H]4CC=C5C[C@@H](O)CC[C@]5(C)[C@H]4CC[C@]23C)O[C@]11CCC[C@@](O)(CO)O1

> <INCHI_IDENTIFIER>
InChI=1S/C27H42O5/c1-16-23-22(31-27(16)10-4-9-26(30,15-28)32-27)14-21-19-6-5-17-13-18(29)7-11-24(17,2)20(19)8-12-25(21,23)3/h5,16,18-23,28-30H,4,6-15H2,1-3H3/t16-,18-,19+,20-,21+,22-,23-,24-,25-,26-,27-/m0/s1

> <INCHI_KEY>
YYHKEZLLHMMPDQ-QCKYGXJNSA-N

> <FORMULA>
C27H42O5

> <MOLECULAR_WEIGHT>
446.628

> <EXACT_MASS>
446.303224452

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
51.68733853295669

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'S,2S,2'R,4'S,6S,7'S,8'R,9'S,12'S,13'R,16'S)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-18'-ene-6,16'-diol

> <JCHEM_LOGP>
3.513612178000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.4767981147418

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.247429120337324

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3964792180480456

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
123.33449999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1'S,2S,2'R,4'S,6S,7'S,8'R,9'S,12'S,13'R,16'S)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-18'-ene-6,16'-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0      13.454  -7.989   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.686  -6.467   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.054  -5.760   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.805  -4.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.173  -3.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.268  -4.616   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.805  -4.526   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      19.497  -3.150   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.034  -3.061   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.880  -4.347   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.418  -4.258   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.264  -5.545   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      25.801  -5.455   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      23.573  -6.921   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.035  -7.010   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      21.189  -5.724   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      20.498  -7.100   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      19.652  -5.813   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      18.960  -7.189   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      17.423  -7.279   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      16.577  -5.992   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      15.746  -7.289   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      13.282  -4.008   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      12.591  -5.384   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      12.048  -6.825   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.528  -7.075   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.552  -5.884   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.095  -4.443   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       8.582  -4.158   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      10.113  -2.903   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.789  -2.118   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      11.615  -4.193   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   24                                                  
CONECT    3    2    4   21                                                  
CONECT    4    3    5   23                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   21                                                  
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   10   17   18                                             
CONECT   17   16                                                            
CONECT   18   16    7   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20    6    3   22                                             
CONECT   22   21                                                            
CONECT   23    4   24                                                       
CONECT   24   23    2   25   32                                             
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30   32                                             
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30                                                            
CONECT   32   28   24                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₂O₅

Average Mass

446.6280 Da

Monoisotopic Mass

446.30322 Da

IUPAC Name

(1'S,2S,2'R,4'S,6S,7'S,8'R,9'S,12'S,13'R,16'S)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-18'-ene-6,16'-diol

Traditional Name

(1'S,2S,2'R,4'S,6S,7'S,8'R,9'S,12'S,13'R,16'S)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-18'-ene-6,16'-diol

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](C[C@@H]3[C@@H]4CC=C5C[C@@H](O)CC[C@]5(C)[C@H]4CC[C@]23C)O[C@]11CCC[C@@](O)(CO)O1

InChI Identifier

InChI=1S/C27H42O5/c1-16-23-22(31-27(16)10-4-9-26(30,15-28)32-27)14-21-19-6-5-17-13-18(29)7-11-24(17,2)20(19)8-12-25(21,23)3/h5,16,18-23,28-30H,4,6-15H2,1-3H3/t16-,18-,19+,20-,21+,22-,23-,24-,25-,26-,27-/m0/s1

InChI Key

YYHKEZLLHMMPDQ-QCKYGXJNSA-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
Tacca leontopetaloides	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Prostaglandins and related compounds

Alternative Parents

Substituents

Prostaglandin skeleton
3-hydroxy-delta-5-steroid
3-hydroxysteroid
Hydroxysteroid
3-beta-hydroxysteroid
3-beta-hydroxy-delta-5-steroid
Delta-5-steroid
Steroid
Ketal
Oxane
Cyclic alcohol
Tetrahydrofuran
Hemiacetal
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Hydrocarbon derivative
Organooxygen compound
Organic oxygen compound
Alcohol
Primary alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	3.51	ChemAxon
pKa (Strongest Acidic)	11.25	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.15 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	123.33 m³·mol⁻¹	ChemAxon
Polarizability	51.69 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162844287

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol (NP0196656)

MOL for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

3D MOL for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

3D SDF for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

3D-SDF for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

PDB for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

3D PDB for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

SMILES for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

INCHI for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

Structure for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)

3D Structure for NP0196656 ((1's,2s,2'r,4's,6s,7's,8'r,9's,12's,13'r,16's)-6-(hydroxymethyl)-7',9',13'-trimethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan]-18'-ene-6,16'-diol)