NP-MRD: Showing NP-Card for (1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid (NP0167479)

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Record Information

Version

1.0

Created at

2022-09-03 03:03:59 UTC

Updated at

2022-09-03 03:04:00 UTC

NP-MRD ID

NP0167479

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid

Description

(25S)-6beta-Hydroxy-2,3-seco-5alpha-spirostane-2,3-dioic acid 3,6-lactone belongs to the class of organic compounds known as naphthofurans. Naphthofurans are compounds containing a furan ring fused to a naphthalene moiety. Furan is a 5 membered- ring aromatic ring with four carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings. (1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid is found in Allium obliquum. Based on a literature review very few articles have been published on (25S)-6beta-Hydroxy-2,3-seco-5alpha-spirostane-2,3-dioic acid 3,6-lactone.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032205042D          

 33 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309032205042D          

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 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 19 18  1  1  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  6  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 20 26  1  0  0  0  0
 12 26  1  0  0  0  0
 26 27  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 11 29  1  0  0  0  0
 29 30  1  1  0  0  0
 31 29  1  1  0  0  0
  9 31  1  0  0  0  0
 31 32  1  0  0  0  0
  5 32  1  0  0  0  0
 32 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0167479

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4C[C@H]5OC(=O)C[C@H]5[C@](C)(CC(O)=O)[C@H]4CC[C@]23C)O[C@]11CC[C@H](C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C27H40O6/c1-14-5-8-27(31-13-14)15(2)24-21(33-27)10-18-16-9-20-19(11-23(30)32-20)26(4,12-22(28)29)17(16)6-7-25(18,24)3/h14-21,24H,5-13H2,1-4H3,(H,28,29)/t14-,15-,16+,17-,18-,19+,20+,21-,24-,25-,26+,27+/m0/s1

> <INCHI_KEY>
OTCSBULKTTUVHL-VXFQDUCJSA-N

> <FORMULA>
C27H40O6

> <MOLECULAR_WEIGHT>
460.611

> <EXACT_MASS>
460.282489008

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
51.59826904765676

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(1'R,2R,2'S,4'S,5S,7'S,8'R,9'S,12'S,13'R,14'S,18'R)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0^{2,9}.0^{4,8}.0^{14,18}]nonadecane]-13'-yl]acetic acid

> <ALOGPS_LOGP>
3.47

> <JCHEM_LOGP>
3.8985521626666673

> <ALOGPS_LOGS>
-5.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.295517009752346

> <JCHEM_PKA_STRONGEST_BASIC>
-4.048869534876462

> <JCHEM_POLAR_SURFACE_AREA>
82.06

> <JCHEM_REFRACTIVITY>
120.9797

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.22e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2R,2'S,4'S,5S,7'S,8'R,9'S,12'S,13'R,14'S,18'R)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0^{2,9}.0^{4,8}.0^{14,18}]nonadecane]-13'-ylacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.085  -8.381   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.453  -8.468   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.297  -7.180   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.834  -7.267   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.528  -8.642   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.684  -9.930   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.146  -9.843   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.502  -7.449   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.937  -8.007   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.426  -7.615   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.260  -8.910   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.780  -9.157   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.754  -7.964   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.274  -8.211   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      13.475  -7.247   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      14.763  -8.091   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      16.203  -7.545   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      14.358  -9.577   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.820  -9.651   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.846 -10.844   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.190 -11.596   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.338 -12.298   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.344 -13.464   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      13.857 -13.177   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      11.837 -14.918   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.326 -10.597   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.352 -11.789   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.832 -11.542   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.286 -10.102   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.192 -11.187   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.850  -9.545   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.361  -9.937   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.803 -11.373   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8   32                                             
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5    9                                                       
CONECT    9    8   10   31                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   29                                                  
CONECT   12   11   13   26                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   14   20                                                  
CONECT   20   19   21   22   26                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   20   12   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   11   30   31                                             
CONECT   30   29                                                            
CONECT   31   29    9   32                                                  
CONECT   32   31    5   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   76    0
END

View in JSmol

Synonyms

Value	Source
(25S)-6b-Hydroxy-2,3-seco-5a-spirostane-2,3-dioate 3,6-lactone	Generator
(25S)-6b-Hydroxy-2,3-seco-5a-spirostane-2,3-dioic acid 3,6-lactone	Generator
(25S)-6beta-Hydroxy-2,3-seco-5alpha-spirostane-2,3-dioate 3,6-lactone	Generator
(25S)-6Β-hydroxy-2,3-seco-5α-spirostane-2,3-dioate 3,6-lactone	Generator
(25S)-6Β-hydroxy-2,3-seco-5α-spirostane-2,3-dioic acid 3,6-lactone	Generator

Chemical Formula

C₂₇H₄₀O₆

Average Mass

460.6110 Da

Monoisotopic Mass

460.28249 Da

IUPAC Name

2-[(1'R,2R,2'S,4'S,5S,7'S,8'R,9'S,12'S,13'R,14'S,18'R)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0^{2,9}.0^{4,8}.0^{14,18}]nonadecane]-13'-yl]acetic acid

Traditional Name

(1'R,2R,2'S,4'S,5S,7'S,8'R,9'S,12'S,13'R,14'S,18'R)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0^{2,9}.0^{4,8}.0^{14,18}]nonadecane]-13'-ylacetic acid

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4C[C@H]5OC(=O)C[C@H]5[C@](C)(CC(O)=O)[C@H]4CC[C@]23C)O[C@]11CC[C@H](C)CO1

InChI Identifier

InChI=1S/C27H40O6/c1-14-5-8-27(31-13-14)15(2)24-21(33-27)10-18-16-9-20-19(11-23(30)32-20)26(4,12-22(28)29)17(16)6-7-25(18,24)3/h14-21,24H,5-13H2,1-4H3,(H,28,29)/t14-,15-,16+,17-,18-,19+,20+,21-,24-,25-,26+,27+/m0/s1

InChI Key

OTCSBULKTTUVHL-VXFQDUCJSA-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
Allium obliquum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthofurans. Naphthofurans are compounds containing a furan ring fused to a naphthalene moiety. Furan is a 5 membered- ring aromatic ring with four carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthofurans

Sub Class

Not Available

Direct Parent

Naphthofurans

Alternative Parents

Substituents

Naphthofuran
Ketal
Dicarboxylic acid or derivatives
Gamma butyrolactone
Oxane
Oxolane
Carboxylic acid ester
Lactone
Carboxylic acid
Acetal
Carboxylic acid derivative
Oxacycle
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Organooxygen compound
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	3.47	ALOGPS
logP	3.9	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	4.3	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	82.06 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	120.98 m³·mol⁻¹	ChemAxon
Polarizability	51.6 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

101699863

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid (NP0167479)

MOL for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

3D MOL for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

3D SDF for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

3D-SDF for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

PDB for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

3D PDB for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

SMILES for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

INCHI for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

Structure for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)

3D Structure for NP0167479 ((1'r,2r,2's,4's,5s,7's,8'r,9's,12's,13'r,14's,18'r)-5,7',9',13'-tetramethyl-16'-oxo-5',17'-dioxaspiro[oxane-2,6'-pentacyclo[10.7.0.0²,⁹.0⁴,⁸.0¹⁴,¹⁸]nonadecan]-13'-ylacetic acid)