NP-MRD: Showing NP-Card for Rumphioside I (NP0331665)

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Record Information

Version

2.0

Created at

2023-05-31 12:01:45 UTC

Updated at

2024-09-03 04:16:25 UTC

NP-MRD ID

NP0331665

Natural Product DOI

https://doi.org/10.57994/0657

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rumphioside I

Description

Rumphioside I belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol. Rumphioside I was first documented in 2023 (PMID: 37200063). Based on a literature review very few articles have been published on Rumphioside I.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032214492D          

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  5 38  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309032214492D          

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    2.6122    0.0467    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0408    0.7444    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0694    1.5689    0.0000 C   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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 16 15  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 16 25  1  0  0  0  0
 25 26  1  6  0  0  0
 14 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 27 31  2  0  0  0  0
 11 32  1  0  0  0  0
 32 33  1  6  0  0  0
 34 33  1  6  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 32 36  1  0  0  0  0
 36 37  2  0  0  0  0
 34 38  1  0  0  0  0
  5 38  1  0  0  0  0
 10 38  1  0  0  0  0
 38 39  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0331665

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=C[C@H](O)C[C@H]2[C@](C)(CC(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C3=COC=C3)[C@H]3C[C@H](OC3=O)[C@@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C27H36O12/c1-26(9-16(12-4-5-36-11-12)37-25-22(32)21(31)20(30)17(10-28)38-25)14-8-19(39-24(14)34)27(2)15(23(33)35-3)6-13(29)7-18(26)27/h4-6,11,13-14,16-22,25,28-32H,7-10H2,1-3H3/t13-,14-,16?,17+,18-,19-,20+,21-,22+,25+,26+,27-/m0/s1

> <INCHI_KEY>
GMZIBNWBLDPKAJ-KSABOFSBSA-N

> <FORMULA>
C27H36O12

> <MOLECULAR_WEIGHT>
552.573

> <EXACT_MASS>
552.220676599

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
54.993202612334564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1S,2R,5R,7S,8S,9R)-8-[2-(furan-3-yl)-2-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl]-5-hydroxy-2,8-dimethyl-10-oxo-11-oxatricyclo[7.2.1.0^{2,7}]dodec-3-ene-3-carboxylate

> <ALOGPS_LOGP>
-0.01

> <JCHEM_LOGP>
-0.40653183599999976

> <ALOGPS_LOGS>
-2.68

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.190367613862492

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.208978770703936

> <JCHEM_PKA_STRONGEST_BASIC>
-2.862014352984099

> <JCHEM_POLAR_SURFACE_AREA>
185.35

> <JCHEM_REFRACTIVITY>
131.0046

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.14e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1S,2R,5R,7S,8S,9R)-8-[2-(furan-3-yl)-2-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl]-5-hydroxy-2,8-dimethyl-10-oxo-11-oxatricyclo[7.2.1.0^{2,7}]dodec-3-ene-3-carboxylate

> <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      -2.070   6.273   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -2.239   4.743   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.997   3.832   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.413   4.451   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.165   2.301   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.575   1.681   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.744   0.150   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.153  -0.469   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.502  -0.761   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.092  -0.141   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.000  -1.227   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.302  -2.050   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.512  -2.679   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.511  -3.849   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.023  -5.302   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.022  -6.472   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.492  -6.189   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -2.493  -7.359   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.007  -7.077   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -4.520  -5.625   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -1.981  -8.811   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -2.982  -9.981   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.467  -9.094   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.046 -10.546   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.535  -7.924   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.048  -8.206   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.003  -3.567   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.121  -4.626   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.474  -3.890   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.192  -2.376   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -1.665  -2.176   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.530  -1.051   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.362   0.725   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.378   2.212   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.833   1.708   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       3.345   0.256   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       4.876   0.087   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       0.076   1.390   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.130   2.929   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   38                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   38                                                  
CONECT   11   10   12   13   32                                             
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   27                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   16   26                                                  
CONECT   26   25                                                            
CONECT   27   14   28   31                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   27                                                       
CONECT   32   11   33   36                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   38                                                  
CONECT   35   34   36                                                       
CONECT   36   35   32   37                                                  
CONECT   37   36                                                            
CONECT   38   34    5   10   39                                             
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₆O₁₂

Average Mass

552.5730 Da

Monoisotopic Mass

552.22068 Da

IUPAC Name

methyl (1S,2R,5R,7S,8S,9R)-8-[2-(furan-3-yl)-2-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}ethyl]-5-hydroxy-2,8-dimethyl-10-oxo-11-oxatricyclo[7.2.1.0^{2,7}]dodec-3-ene-3-carboxylate

Traditional Name

CAS Registry Number

Not Available

SMILES

COC(=O)C1=C[C@H](O)C[C@H]2[C@](C)(CC(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C3=COC=C3)[C@H]3C[C@H](OC3=O)[C@@]12C

InChI Identifier

InChI=1S/C27H36O12/c1-26(9-16(12-4-5-36-11-12)37-25-22(32)21(31)20(30)17(10-28)38-25)14-8-19(39-24(14)34)27(2)15(23(33)35-3)6-13(29)7-18(26)27/h4-6,11,13-14,16-22,25,28-32H,7-10H2,1-3H3/t13-,14-,16?,17+,18-,19-,20+,21-,22+,25+,26+,27-/m0/s1

InChI Key

GMZIBNWBLDPKAJ-KSABOFSBSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

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

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400, CD₃OD, simulated)	Not Available	Not Available	Not Available	2024-05-11	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
crispa		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl glycosides

Direct Parent

Fatty acyl glycosides of mono- and disaccharides

Alternative Parents

Substituents

Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Caprolactone
Oxepane
Dicarboxylic acid or derivatives
Gamma butyrolactone
Monosaccharide
Oxane
Oxolane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Heteroaromatic compound
Furan
Secondary alcohol
Lactone
Carboxylic acid ester
Polyol
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Acetal
Organooxygen compound
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Primary alcohol
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	-0.01	ALOGPS
logP	-0.41	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	185.35 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	131 m³·mol⁻¹	ChemAxon
Polarizability	54.99 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

8778151

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10602782

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Rumphioside I (NP0331665)

MOL for NP0331665 (Rumphioside I)

3D MOL for NP0331665 (Rumphioside I)

3D SDF for NP0331665 (Rumphioside I)

3D-SDF for NP0331665 (Rumphioside I)

PDB for NP0331665 (Rumphioside I)

3D PDB for NP0331665 (Rumphioside I)

SMILES for NP0331665 (Rumphioside I)

INCHI for NP0331665 (Rumphioside I)

Structure for NP0331665 (Rumphioside I)

3D Structure for NP0331665 (Rumphioside I)