NP-MRD: Showing NP-Card for Cynatratoside A (NP0137594)

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Record Information

Version

2.0

Created at

2022-05-30 16:57:12 UTC

Updated at

2022-05-30 16:57:12 UTC

NP-MRD ID

NP0137594

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cynatratoside A

Description

8-[(5-Hydroxy-4-methoxy-6-methyloxan-2-yl)oxy]-5,19-dimethyl-15,18,20-trioxapentacyclo[14.5.1.0⁴,¹³.0⁵,¹⁰.0¹⁹,²²]Docosa-1(21),10-dien-14-one belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Cynatratoside A is found in Vincetoxicum amplexicaule, Vincetoxicum atratum and Vincetoxicum forrestii. 8-[(5-Hydroxy-4-methoxy-6-methyloxan-2-yl)oxy]-5,19-dimethyl-15,18,20-trioxapentacyclo[14.5.1.0⁴,¹³.0⁵,¹⁰.0¹⁹,²²]Docosa-1(21),10-dien-14-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004161503082D          

 36 41  0  0  0  0            999 V2000
    9.8566    2.0382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2890    0.5042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1533004161503082D          

 36 41  0  0  0  0            999 V2000
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  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 12 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 10 29  1  0  0  0  0
 29 30  1  0  0  0  0
  7 30  1  0  0  0  0
 22 31  1  0  0  0  0
 15 31  1  0  0  0  0
 18 31  1  0  0  0  0
  5 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0137594

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1CC(OC2CCC3(C)C4CCC5=COC6(C)OCC(OC(=O)C4CC=C3C2)C56)OC(C)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O8/c1-15-25(29)21(31-4)12-23(34-15)35-18-9-10-27(2)17(11-18)6-7-19-20(27)8-5-16-13-32-28(3)24(16)22(14-33-28)36-26(19)30/h6,13,15,18-25,29H,5,7-12,14H2,1-4H3

> <INCHI_KEY>
QANVGLGBLJFUIP-UHFFFAOYSA-N

> <FORMULA>
C28H40O8

> <MOLECULAR_WEIGHT>
504.62

> <EXACT_MASS>
504.272318248

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
55.63217131627519

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8-[(5-hydroxy-4-methoxy-6-methyloxan-2-yl)oxy]-5,19-dimethyl-15,18,20-trioxapentacyclo[14.5.1.0⁴,¹³.0⁵,¹⁰.0¹⁹,²²]docosa-1(21),10-dien-14-one

> <ALOGPS_LOGP>
3.20

> <JCHEM_LOGP>
2.9808757013333307

> <ALOGPS_LOGS>
-4.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.215144980908246

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5794955853507338

> <JCHEM_POLAR_SURFACE_AREA>
92.68

> <JCHEM_REFRACTIVITY>
130.22920000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.91e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-[(5-hydroxy-4-methoxy-6-methyloxan-2-yl)oxy]-5,19-dimethyl-15,18,20-trioxapentacyclo[14.5.1.0⁴,¹³.0⁵,¹⁰.0¹⁹,²²]docosa-1(21),10-dien-14-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0      18.399   3.805   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      17.485   2.565   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      15.955   2.736   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.041   1.496   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.511   1.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      12.598   0.428   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      11.067   0.599   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.154  -0.641   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.623  -0.470   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.006   0.941   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.093  -0.299   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.476   1.112   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.041  -0.365   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.759  -1.218   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.228  -1.046   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.323  -2.418   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.832  -2.036   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       0.734  -0.499   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.697  -1.066   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.248   0.687   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.577   1.988   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.069   1.605   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.982   2.845   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.479   3.208   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.650   4.738   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       5.859   2.523   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.772   3.763   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.303   3.592   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.920   2.181   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.450   2.010   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.166   0.068   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      12.894   3.078   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      13.808   4.318   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.191   5.729   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      15.338   4.147   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      16.251   5.387   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   32                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   30                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12   29                                             
CONECT   11   10                                                            
CONECT   12   10   13   26                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   31                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20   31                                             
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   31                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   12   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   10   30                                                  
CONECT   30   29    7                                                       
CONECT   31   22   15   18                                                  
CONECT   32    5   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    3   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   82    0
END

View in JSmol

Synonyms

Value	Source
Cynatratoside a	MeSH

Chemical Formula

C₂₈H₄₀O₈

Average Mass

504.6200 Da

Monoisotopic Mass

504.27232 Da

IUPAC Name

8-[(5-hydroxy-4-methoxy-6-methyloxan-2-yl)oxy]-5,19-dimethyl-15,18,20-trioxapentacyclo[14.5.1.0⁴,¹³.0⁵,¹⁰.0¹⁹,²²]docosa-1(21),10-dien-14-one

Traditional Name

8-[(5-hydroxy-4-methoxy-6-methyloxan-2-yl)oxy]-5,19-dimethyl-15,18,20-trioxapentacyclo[14.5.1.0⁴,¹³.0⁵,¹⁰.0¹⁹,²²]docosa-1(21),10-dien-14-one

CAS Registry Number

Not Available

SMILES

COC1CC(OC2CCC3(C)C4CCC5=COC6(C)OCC(OC(=O)C4CC=C3C2)C56)OC(C)C1O

InChI Identifier

InChI=1S/C28H40O8/c1-15-25(29)21(31-4)12-23(34-15)35-18-9-10-27(2)17(11-18)6-7-19-20(27)8-5-16-13-32-28(3)24(16)22(14-33-28)36-26(19)30/h6,13,15,18-25,29H,5,7-12,14H2,1-4H3

InChI Key

QANVGLGBLJFUIP-UHFFFAOYSA-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
Vincetoxicum amplexicaule	LOTUS Database	35616633
Vincetoxicum atratum	LOTUS Database	35616633
Vincetoxicum forrestii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Hexose monosaccharide
O-glycosyl compound
Furofuran
Ketal
Monosaccharide
Oxane
Dihydrofuran
Tetrahydrofuran
Carboxylic acid ester
Lactone
Secondary alcohol
Oxacycle
Ether
Dialkyl ether
Acetal
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
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	3.2	ALOGPS
logP	2.98	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	13.22	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	92.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	130.23 m³·mol⁻¹	ChemAxon
Polarizability	55.63 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

175701

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cynatratoside A (NP0137594)

MOL for NP0137594 (Cynatratoside A)

3D MOL for NP0137594 (Cynatratoside A)

3D SDF for NP0137594 (Cynatratoside A)

3D-SDF for NP0137594 (Cynatratoside A)

PDB for NP0137594 (Cynatratoside A)

3D PDB for NP0137594 (Cynatratoside A)

SMILES for NP0137594 (Cynatratoside A)

INCHI for NP0137594 (Cynatratoside A)

Structure for NP0137594 (Cynatratoside A)

3D Structure for NP0137594 (Cynatratoside A)