NP-MRD: Showing NP-Card for rac-5,6-Epoxy-retinoyl-beta-D-glucuronide (NP0092350)

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Record Information

Version

2.0

Created at

2022-05-11 19:04:16 UTC

Updated at

2022-05-11 19:04:16 UTC

NP-MRD ID

NP0092350

Secondary Accession Numbers

None

Natural Product Identification

Common Name

rac-5,6-Epoxy-retinoyl-beta-D-glucuronide

Description

Rac-5,6-Epoxy-retinoyl-beta-D-glucuronide belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. Rac-5,6-Epoxy-retinoyl-beta-D-glucuronide is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303102016592D          

 35 37  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652303102016592D          

 35 37  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0092350

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(\C=C\[C@]12O[C@]1(C)CCCC2(C)C)=C/C=C/C(/C)=C/C(=O)O[C@@H]1O[C@H]([C@@H](O)[C@@H](O)[C@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H36O9/c1-15(10-13-26-24(3,4)11-7-12-25(26,5)35-26)8-6-9-16(2)14-17(27)33-23-20(30)18(28)19(29)21(34-23)22(31)32/h6,8-10,13-14,18-21,23,28-30H,7,11-12H2,1-5H3,(H,31,32)/b9-6+,13-10+,15-8+,16-14+/t18-,19+,20-,21-,23-,25-,26-/m1/s1

> <INCHI_KEY>
BZPOQLONXBJGAZ-XSHYMXFSSA-N

> <FORMULA>
C26H36O9

> <MOLECULAR_WEIGHT>
492.5586

> <EXACT_MASS>
492.23593275

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
52.91647571379657

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5R,6S)-6-{[(2E,4E,6E,8E)-3,7-dimethyl-9-[(1R,6R)-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]nona-2,4,6,8-tetraenoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
3.14

> <JCHEM_LOGP>
2.826110027333333

> <ALOGPS_LOGS>
-4.03

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.212250468844253

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3892099259499915

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6869063371000665

> <JCHEM_POLAR_SURFACE_AREA>
146.05

> <JCHEM_REFRACTIVITY>
128.82109999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.64e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5R,6S)-6-{[(2E,4E,6E,8E)-3,7-dimethyl-9-[(1R,6R)-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]nona-2,4,6,8-tetraenoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0       0.357   7.081   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.357  12.416   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.991   5.030   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.011   5.030   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.897   0.206   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.897   9.748   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   8.415   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  11.082   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   5.747   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.897   4.414   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  13.749   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.897   7.081   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.897  12.416   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.897  15.083   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.897  20.418   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.357  20.418   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  19.084   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.413  19.084   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.953  19.084   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.897  17.751   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.357  15.083   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       2.667  21.752   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -0.413  21.752   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       4.207  19.084   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -2.723  17.751   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -2.723  20.418   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       2.667  16.417   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       0.357  17.751   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2   16                                                            
CONECT    3   24                                                            
CONECT    4   24                                                            
CONECT    5   25                                                            
CONECT    6    8    9                                                       
CONECT    7   11   12                                                       
CONECT    8    6   15                                                       
CONECT    9    6   16                                                       
CONECT   10   13   15                                                       
CONECT   11    7   24                                                       
CONECT   12    7   25                                                       
CONECT   13   10   26                                                       
CONECT   14   16   17                                                       
CONECT   15    1    8   10                                                  
CONECT   16    2    9   14                                                  
CONECT   17   14   27   33                                                  
CONECT   18   19   20   28                                                  
CONECT   19   18   21   29                                                  
CONECT   20   18   23   30                                                  
CONECT   21   19   22   34                                                  
CONECT   22   21   31   32                                                  
CONECT   23   20   33   34                                                  
CONECT   24    3    4   11   26                                             
CONECT   25    5   12   26   35                                             
CONECT   26   13   24   25   35                                             
CONECT   27   17                                                            
CONECT   28   18                                                            
CONECT   29   19                                                            
CONECT   30   20                                                            
CONECT   31   22                                                            
CONECT   32   22                                                            
CONECT   33   17   23                                                       
CONECT   34   21   23                                                       
CONECT   35   25   26                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Value	Source
rac-5,6-Epoxy-retinoyl-b-D-glucuronide	Generator
rac-5,6-Epoxy-retinoyl-β-D-glucuronide	Generator

Chemical Formula

C₂₆H₃₆O₉

Average Mass

492.5586 Da

Monoisotopic Mass

492.23593 Da

IUPAC Name

(2R,3S,4R,5R,6S)-6-{[(2E,4E,6E,8E)-3,7-dimethyl-9-[(1R,6R)-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]nona-2,4,6,8-tetraenoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

Traditional Name

(2R,3S,4R,5R,6S)-6-{[(2E,4E,6E,8E)-3,7-dimethyl-9-[(1R,6R)-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]nona-2,4,6,8-tetraenoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

C\C(\C=C\[C@]12O[C@]1(C)CCCC2(C)C)=C/C=C/C(/C)=C/C(=O)O[C@@H]1O[C@H]([C@@H](O)[C@@H](O)[C@H]1O)C(O)=O

InChI Identifier

InChI=1S/C26H36O9/c1-15(10-13-26-24(3,4)11-7-12-25(26,5)35-26)8-6-9-16(2)14-17(27)33-23-20(30)18(28)19(29)21(34-23)22(31)32/h6,8-10,13-14,18-21,23,28-30H,7,11-12H2,1-5H3,(H,31,32)/b9-6+,13-10+,15-8+,16-14+/t18-,19+,20-,21-,23-,25-,26-/m1/s1

InChI Key

BZPOQLONXBJGAZ-XSHYMXFSSA-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
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Diterpene glycosides

Alternative Parents

Substituents

Diterpene glycoside
Retinoid ester
Diterpenoid
Retinoid skeleton
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Hexose monosaccharide
Beta-hydroxy acid
Fatty acid ester
Oxepane
Dicarboxylic acid or derivatives
Fatty acyl
Hydroxy acid
Monosaccharide
Oxane
Pyran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Polyol
Organoheterocyclic compound
Oxacycle
Ether
Oxirane
Acetal
Dialkyl ether
Carboxylic acid
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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	3.14	ALOGPS
logP	2.83	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	146.05 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	128.82 m³·mol⁻¹	ChemAxon
Polarizability	52.92 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0060123

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB034576

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

131769835

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for rac-5,6-Epoxy-retinoyl-beta-D-glucuronide (NP0092350)

MOL for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

3D MOL for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

3D SDF for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

3D-SDF for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

PDB for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

3D PDB for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

SMILES for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

INCHI for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

Structure for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)

3D Structure for NP0092350 (rac-5,6-Epoxy-retinoyl-beta-D-glucuronide)