NP-MRD: Showing NP-Card for (+)-Sinocrassoside D1 (NP0072318)

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Record Information

Version

2.0

Created at

2022-04-28 17:40:40 UTC

Updated at

2022-04-28 17:40:40 UTC

NP-MRD ID

NP0072318

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Sinocrassoside D1

Description

(2S,3R,4R,5S,6S)-2-{[2-(3,4-dihydroxyphenyl)-3,5,8-trihydroxy-4-oxo-4H-chromen-7-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl (2S)-2-methylbutanoate belongs to the class of organic compounds known as flavonoid-7-o-glycosides. (+)-Sinocrassoside D1 is found in Sinocrassula indica . These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C7-position (2S,3R,4R,5S,6S)-2-{[2-(3,4-dihydroxyphenyl)-3,5,8-trihydroxy-4-oxo-4H-chromen-7-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl (2S)-2-methylbutanoate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309272006312D          

 39 42  0  0  0  0            999 V2000
 9999.8428 9999.8176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.2658 9996.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.410610001.0508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.837610000.2259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4154 9998.9906    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.9866 9999.8155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.5579 9998.9906    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.8435 9998.5765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.1271 9998.9906    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9993.4127 9998.5765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9992.6984 9998.9906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.1271 9999.8155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.8435 9997.7516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.9866 9996.5153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.5579 9997.3402    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 9999.8405 9997.3359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.2671 9998.9860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.5526 9998.5736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  7  8  1  0  0  0  0
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  1 29  1  0  0  0  0
 36  2  2  0  0  0  0
 24  3  1  0  0  0  0
 23  4  1  0  0  0  0
 32 16  1  0  0  0  0
 30  5  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309272006312D          

 39 42  0  0  0  0            999 V2000
 9999.8428 9999.8176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 34  1  0  0  0  0
 33 38  1  0  0  0  0
 38 26  1  0  0  0  0
 34 29  2  0  0  0  0
 32 35  2  0  0  0  0
 39 37  1  0  0  0  0
  1 29  1  0  0  0  0
 36  2  2  0  0  0  0
 24  3  1  0  0  0  0
 23  4  1  0  0  0  0
 32 16  1  0  0  0  0
 30  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0072318

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)C(=O)O[C@@H]1[C@@H](O)[C@H](C)O[C@@H](OC2=CC(O)=C3C(=O)C(O)=C(OC3=C2O)C2=CC(O)=C(O)C=C2)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O13/c1-4-9(2)25(35)39-24-17(30)10(3)36-26(21(24)34)37-15-8-14(29)16-19(32)20(33)22(38-23(16)18(15)31)11-5-6-12(27)13(28)7-11/h5-10,17,21,24,26-31,33-34H,4H2,1-3H3/t9-,10-,17-,21+,24+,26-/m0/s1

> <INCHI_KEY>
FFERJMKECZZBSZ-GCVRPTKUSA-N

> <FORMULA>
C26H28O13

> <MOLECULAR_WEIGHT>
548.497

> <EXACT_MASS>
548.152990962

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
54.47216929245386

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,5S,6S)-2-{[2-(3,4-dihydroxyphenyl)-3,5,8-trihydroxy-4-oxo-4H-chromen-7-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl (2S)-2-methylbutanoate

> <ALOGPS_LOGP>
2.95

> <JCHEM_LOGP>
2.760792216333334

> <ALOGPS_LOGS>
-2.78

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.475071064716579

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.521555934833315

> <JCHEM_PKA_STRONGEST_BASIC>
-3.626998643146826

> <JCHEM_POLAR_SURFACE_AREA>
212.66999999999996

> <JCHEM_REFRACTIVITY>
132.3977

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.10e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,5S,6S)-2-{[2-(3,4-dihydroxyphenyl)-3,5,8-trihydroxy-4-oxochromen-7-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl (2S)-2-methylbutanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  O   UNK     0    8666.3738666.326   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8669.0308660.143   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8673.0338668.628   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8675.6978667.088   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8663.7098664.782   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8661.0428666.322   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8658.3758664.782   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8657.0418664.009   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8655.7048664.782   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8654.3708664.009   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8653.0378664.782   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8655.7048666.322   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0    8657.0418662.470   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0    8661.0428660.162   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0    8658.3758661.702   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0    8666.3738660.143   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0    8661.0428664.780   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8659.7088664.010   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8659.7088662.470   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8661.0428661.701   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0    8662.3758662.470   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0    8662.3758664.010   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8674.3668666.322   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8673.0328667.092   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8671.6998666.322   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8671.6998664.782   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8673.0328664.012   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8674.3668664.782   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8666.3698664.774   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0    8665.0358664.004   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8665.0358662.464   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8666.3698661.694   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0    8669.0328664.774   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0    8667.6988664.004   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0    8667.6988662.464   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0    8669.0328661.694   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0    8670.3668662.464   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0    8670.3668664.004   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0    8671.6968661.688   0.000  0.00  0.00           O+0
CONECT    1   29                                                            
CONECT    2   36                                                            
CONECT    3   24                                                            
CONECT    4   23                                                            
CONECT    5   22   30                                                       
CONECT    6   17                                                            
CONECT    7    8   18                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9                                                            
CONECT   13    8                                                            
CONECT   14   20                                                            
CONECT   15   19                                                            
CONECT   16   32                                                            
CONECT   17   18   22    6                                                  
CONECT   18   17   19    7                                                  
CONECT   19   18   20   15                                                  
CONECT   20   19   21   14                                                  
CONECT   21   20   22                                                       
CONECT   22   17   21    5                                                  
CONECT   23   24   28    4                                                  
CONECT   24   23   25    3                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   38                                                  
CONECT   27   26   28                                                       
CONECT   28   27   23                                                       
CONECT   29   30   34    1                                                  
CONECT   30   29   31    5                                                  
CONECT   31   30   32                                                       
CONECT   32   31   35   16                                                  
CONECT   33   34   38                                                       
CONECT   34   35   33   29                                                  
CONECT   35   34   36   32                                                  
CONECT   36   35   37    2                                                  
CONECT   37   36   38   39                                                  
CONECT   38   37   33   26                                                  
CONECT   39   37                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Value	Source
(2S,3R,4R,5S,6S)-2-{[2-(3,4-dihydroxyphenyl)-3,5,8-trihydroxy-4-oxo-4H-chromen-7-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl (2S)-2-methylbutanoic acid	Generator

Chemical Formula

C₂₆H₂₈O₁₃

Average Mass

548.4970 Da

Monoisotopic Mass

548.15299 Da

IUPAC Name

(2S,3R,4R,5S,6S)-2-{[2-(3,4-dihydroxyphenyl)-3,5,8-trihydroxy-4-oxo-4H-chromen-7-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl (2S)-2-methylbutanoate

Traditional Name

(2S,3R,4R,5S,6S)-2-{[2-(3,4-dihydroxyphenyl)-3,5,8-trihydroxy-4-oxochromen-7-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl (2S)-2-methylbutanoate

CAS Registry Number

Not Available

SMILES

CC[C@H](C)C(=O)O[C@@H]1[C@@H](O)[C@H](C)O[C@@H](OC2=CC(O)=C3C(=O)C(O)=C(OC3=C2O)C2=CC(O)=C(O)C=C2)[C@@H]1O

InChI Identifier

InChI=1S/C26H28O13/c1-4-9(2)25(35)39-24-17(30)10(3)36-26(21(24)34)37-15-8-14(29)16-19(32)20(33)22(38-23(16)18(15)31)11-5-6-12(27)13(28)7-11/h5-10,17,21,24,26-31,33-34H,4H2,1-3H3/t9-,10-,17-,21+,24+,26-/m0/s1

InChI Key

FFERJMKECZZBSZ-GCVRPTKUSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Sinocrassula indica	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid-7-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C7-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-7-O-glycosides

Alternative Parents

Substituents

Flavonoid-7-o-glycoside
3-hydroxyflavone
Hydroxyflavonoid
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
8-hydroxyflavonoid
Flavone
Phenolic glycoside
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Chromone
Benzopyran
1-benzopyran
Catechol
Pyranone
1-hydroxy-4-unsubstituted benzenoid
Phenol
1-hydroxy-2-unsubstituted benzenoid
Fatty acid ester
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Pyran
Oxane
Monosaccharide
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Carboxylic acid ester
Acetal
Monocarboxylic acid or derivatives
Oxacycle
Polyol
Carboxylic acid derivative
Organoheterocyclic compound
Alcohol
Organic oxygen compound
Organic oxide
Carbonyl group
Organooxygen compound
Hydrocarbon derivative
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	2.95	ALOGPS
logP	2.76	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	7.52	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	212.67 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	132.4 m³·mol⁻¹	ChemAxon
Polarizability	54.47 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	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

28285614

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25112364

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (+)-Sinocrassoside D1 (NP0072318)

MOL for NP0072318 ((+)-Sinocrassoside D1)

3D MOL for NP0072318 ((+)-Sinocrassoside D1)

3D SDF for NP0072318 ((+)-Sinocrassoside D1)

3D-SDF for NP0072318 ((+)-Sinocrassoside D1)

PDB for NP0072318 ((+)-Sinocrassoside D1)

3D PDB for NP0072318 ((+)-Sinocrassoside D1)

SMILES for NP0072318 ((+)-Sinocrassoside D1)

INCHI for NP0072318 ((+)-Sinocrassoside D1)

Structure for NP0072318 ((+)-Sinocrassoside D1)

3D Structure for NP0072318 ((+)-Sinocrassoside D1)