NP-MRD: Showing NP-Card for Genipin-1-O-gentiobioside (NP0138770)

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Record Information

Version

1.0

Created at

2022-06-29 18:35:24 UTC

Updated at

2022-06-29 18:35:24 UTC

NP-MRD ID

NP0138770

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Genipin-1-O-gentiobioside

Description

Methyl 7-(hydroxymethyl)-1-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton. Genipin-1-O-gentiobioside is found in Gardenia jasminoides and Genipa americana. Methyl 7-(hydroxymethyl)-1-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004181502232D          

 38 41  0  0  0  0            999 V2000
    4.7079    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 35 36  2  0  0  0  0
 32 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1533004181502232D          

 38 41  0  0  0  0            999 V2000
    4.7079    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 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  1  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
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  0  0  0  0
 12 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 10 30  1  0  0  0  0
 30 31  1  0  0  0  0
  8 32  1  0  0  0  0
 32 33  1  0  0  0  0
  5 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 32 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0138770

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=COC(OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(O)C2O)C2C1CC=C2CO

> <INCHI_IDENTIFIER>
InChI=1S/C23H34O15/c1-33-20(32)10-6-34-21(13-8(4-24)2-3-9(10)13)38-23-19(31)17(29)15(27)12(37-23)7-35-22-18(30)16(28)14(26)11(5-25)36-22/h2,6,9,11-19,21-31H,3-5,7H2,1H3

> <INCHI_KEY>
FYZYXYLPBWLLGI-UHFFFAOYSA-N

> <FORMULA>
C23H34O15

> <MOLECULAR_WEIGHT>
550.51

> <EXACT_MASS>
550.189770395

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
52.78502036117744

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 7-(hydroxymethyl)-1-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

> <ALOGPS_LOGP>
-1.75

> <JCHEM_LOGP>
-3.985566951

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.430613145503347

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.908519633233585

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7354216333590458

> <JCHEM_POLAR_SURFACE_AREA>
234.28999999999996

> <JCHEM_REFRACTIVITY>
120.91990000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.80e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 7-(hydroxymethyl)-1-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-APR-15         0                                  
HETATM    1  C   UNK     0       8.788   3.850   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.454   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.787   4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.454   0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       7.454  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       8.788  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      10.122  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.455  -2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      11.455  -0.770   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      12.789  -0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.789   1.540   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      14.123   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.123   3.850   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      15.456   4.620   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      15.456   1.540   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      16.790   2.310   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      15.456  -0.000   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      16.790  -0.770   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      14.123  -0.770   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      14.123  -2.310   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.122  -4.620   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      11.455  -5.390   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.788  -5.390   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       8.788  -6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       7.454  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.121  -5.390   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       3.877  -3.085   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   33                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   32                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   30                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   26                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   15   25                                                  
CONECT   25   24                                                            
CONECT   26   12   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   10   31                                                  
CONECT   31   30                                                            
CONECT   32    8   33   36                                                  
CONECT   33   32    5   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   32   37                                                  
CONECT   37   36   38                                                       
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Value	Source
Methyl 7-(hydroxymethyl)-1-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-1H,4ah,5H,7ah-cyclopenta[c]pyran-4-carboxylic acid	Generator

Chemical Formula

C₂₃H₃₄O₁₅

Average Mass

550.5100 Da

Monoisotopic Mass

550.18977 Da

IUPAC Name

methyl 7-(hydroxymethyl)-1-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

Traditional Name

methyl 7-(hydroxymethyl)-1-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

CAS Registry Number

29307-60-6

SMILES

COC(=O)C1=COC(OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(O)C2O)C2C1CC=C2CO

InChI Identifier

InChI=1S/C23H34O15/c1-33-20(32)10-6-34-21(13-8(4-24)2-3-9(10)13)38-23-19(31)17(29)15(27)12(37-23)7-35-22-18(30)16(28)14(26)11(5-25)36-22/h2,6,9,11-19,21-31H,3-5,7H2,1H3

InChI Key

FYZYXYLPBWLLGI-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
Gardenia jasminoides	LOTUS Database	35616633
Genipa americana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Iridoid O-glycosides

Alternative Parents

Substituents

Iridoid o-glycoside
Disaccharide
Glycosyl compound
Iridoid-skeleton
O-glycosyl compound
Bicyclic monoterpenoid
Monoterpenoid
Oxane
Enoate ester
Methyl ester
Alpha,beta-unsaturated carboxylic ester
Vinylogous ester
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Polyol
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Acetal
Organic oxide
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Primary alcohol
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	-1.8	ALOGPS
logP	-4	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	11.91	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	234.29 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	120.92 m³·mol⁻¹	ChemAxon
Polarizability	52.79 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

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

14179128

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Genipin-1-O-gentiobioside (NP0138770)

MOL for NP0138770 (Genipin-1-O-gentiobioside)

3D MOL for NP0138770 (Genipin-1-O-gentiobioside)

3D SDF for NP0138770 (Genipin-1-O-gentiobioside)

3D-SDF for NP0138770 (Genipin-1-O-gentiobioside)

PDB for NP0138770 (Genipin-1-O-gentiobioside)

3D PDB for NP0138770 (Genipin-1-O-gentiobioside)

SMILES for NP0138770 (Genipin-1-O-gentiobioside)

INCHI for NP0138770 (Genipin-1-O-gentiobioside)

Structure for NP0138770 (Genipin-1-O-gentiobioside)

3D Structure for NP0138770 (Genipin-1-O-gentiobioside)