NP-MRD: Showing NP-Card for rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate (NP0092351)

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Record Information

Version

2.0

Created at

2022-05-11 19:04:18 UTC

Updated at

2022-05-11 19:04:18 UTC

NP-MRD ID

NP0092351

Secondary Accession Numbers

None

Natural Product Identification

Common Name

rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate

Description

Rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. Rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303102016592D          

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M  END

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M  END


  Mrv1652303102016592D          

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 18  3  1  0  0  0  0
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 20 11  1  0  0  0  0
 20 18  2  0  0  0  0
 21 12  1  0  0  0  0
 21 18  1  0  0  0  0
 23 22  1  0  0  0  0
 24 22  1  0  0  0  0
 25 23  1  0  0  0  0
 25 26  1  1  0  0  0
 27 24  1  0  0  0  0
 28  5  1  0  0  0  0
 28  6  1  0  0  0  0
 28 14  1  0  0  0  0
 28 20  1  0  0  0  0
 29 19  2  0  0  0  0
 22 30  1  1  0  0  0
 23 31  1  1  0  0  0
 24 32  1  1  0  0  0
 33 26  2  0  0  0  0
 34 26  1  0  0  0  0
 35 15  1  0  0  0  0
 35 19  1  0  0  0  0
 21 36  1  1  0  0  0
 27 36  1  6  0  0  0
 37 25  1  0  0  0  0
 37 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0092351

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)OC\C=C(/C)\C=C\C=C(/C)\C=C\C1=C(C)[C@@H](CCC1(C)C)O[C@@H]1O[C@H]([C@@H](O)[C@@H](O)[C@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O9/c1-16(8-7-9-17(2)13-15-35-19(4)29)10-11-20-18(3)21(12-14-28(20,5)6)36-27-24(32)22(30)23(31)25(37-27)26(33)34/h7-11,13,21-25,27,30-32H,12,14-15H2,1-6H3,(H,33,34)/b9-7+,11-10+,16-8+,17-13+/t21-,22-,23+,24-,25-,27-/m1/s1

> <INCHI_KEY>
LFXATGINAILLFU-BSJULFBXSA-N

> <FORMULA>
C28H40O9

> <MOLECULAR_WEIGHT>
520.6118

> <EXACT_MASS>
520.267232878

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
57.556245883275125

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5R,6R)-6-{[(1R)-3-[(1E,3E,5E,7E)-9-(acetyloxy)-3,7-dimethylnona-1,3,5,7-tetraen-1-yl]-2,4,4-trimethylcyclohex-2-en-1-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
3.30

> <JCHEM_LOGP>
2.4538464086666676

> <ALOGPS_LOGS>
-4.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.22712201667854

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5138065613312097

> <JCHEM_PKA_STRONGEST_BASIC>
-3.686507353581458

> <JCHEM_POLAR_SURFACE_AREA>
142.75

> <JCHEM_REFRACTIVITY>
140.8711

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.18e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5R,6R)-6-{[(1R)-3-[(1E,3E,5E,7E)-9-(acetyloxy)-3,7-dimethylnona-1,3,5,7-tetraen-1-yl]-2,4,4-trimethylcyclohex-2-en-1-yl]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      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  13.090   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335  20.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.991   8.110   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.011   8.110   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  11.550   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  10.780   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  13.090   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667  15.400   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.001  16.170   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.667  13.860   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.335  18.480   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -6.668  17.710   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -4.001  17.710   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4   19                                                            
CONECT    5   28                                                            
CONECT    6   28                                                            
CONECT    7    8    9                                                       
CONECT    8    7   16                                                       
CONECT    9    7   17                                                       
CONECT   10   11   16                                                       
CONECT   11   10   20                                                       
CONECT   12   14   21                                                       
CONECT   13   15   17                                                       
CONECT   14   12   28                                                       
CONECT   15   13   35                                                       
CONECT   16    1    8   10                                                  
CONECT   17    2    9   13                                                  
CONECT   18    3   20   21                                                  
CONECT   19    4   29   35                                                  
CONECT   20   11   18   28                                                  
CONECT   21   12   18   36                                                  
CONECT   22   23   24   30                                                  
CONECT   23   22   25   31                                                  
CONECT   24   22   27   32                                                  
CONECT   25   23   26   37                                                  
CONECT   26   25   33   34                                                  
CONECT   27   24   36   37                                                  
CONECT   28    5    6   14   20                                             
CONECT   29   19                                                            
CONECT   30   22                                                            
CONECT   31   23                                                            
CONECT   32   24                                                            
CONECT   33   26                                                            
CONECT   34   26                                                            
CONECT   35   15   19                                                       
CONECT   36   21   27                                                       
CONECT   37   25   27                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   76    0
END

View in JSmol

Synonyms

Value	Source
rac-4-Hydroxy-4-O-(b-D-glucuronide)-all-trans-retinyl acetate	Generator
rac-4-Hydroxy-4-O-(b-D-glucuronide)-all-trans-retinyl acetic acid	Generator
rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetic acid	Generator
rac-4-Hydroxy-4-O-(β-D-glucuronide)-all-trans-retinyl acetate	Generator
rac-4-Hydroxy-4-O-(β-D-glucuronide)-all-trans-retinyl acetic acid	Generator

Chemical Formula

C₂₈H₄₀O₉

Average Mass

520.6118 Da

Monoisotopic Mass

520.26723 Da

IUPAC Name

(2R,3S,4R,5R,6R)-6-{[(1R)-3-[(1E,3E,5E,7E)-9-(acetyloxy)-3,7-dimethylnona-1,3,5,7-tetraen-1-yl]-2,4,4-trimethylcyclohex-2-en-1-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

Traditional Name

(2R,3S,4R,5R,6R)-6-{[(1R)-3-[(1E,3E,5E,7E)-9-(acetyloxy)-3,7-dimethylnona-1,3,5,7-tetraen-1-yl]-2,4,4-trimethylcyclohex-2-en-1-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(=O)OC\C=C(/C)\C=C\C=C(/C)\C=C\C1=C(C)[C@@H](CCC1(C)C)O[C@@H]1O[C@H]([C@@H](O)[C@@H](O)[C@H]1O)C(O)=O

InChI Identifier

InChI=1S/C28H40O9/c1-16(8-7-9-17(2)13-15-35-19(4)29)10-11-20-18(3)21(12-14-28(20,5)6)36-27-24(32)22(30)23(31)25(37-27)26(33)34/h7-11,13,21-25,27,30-32H,12,14-15H2,1-6H3,(H,33,34)/b9-7+,11-10+,16-8+,17-13+/t21-,22-,23+,24-,25-,27-/m1/s1

InChI Key

LFXATGINAILLFU-BSJULFBXSA-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 skeleton
Diterpenoid
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Fatty alcohol ester
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Beta-hydroxy acid
Pyran
Oxane
Monosaccharide
Hydroxy acid
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid ester
Acetal
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Polyol
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Alcohol
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	3.3	ALOGPS
logP	2.45	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	3.51	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	142.75 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	140.87 m³·mol⁻¹	ChemAxon
Polarizability	57.56 Å³	ChemAxon
Number of Rings	2	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

HMDB0060141

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB034577

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

131769845

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate (NP0092351)

MOL for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

3D MOL for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

3D SDF for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

3D-SDF for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

PDB for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

3D PDB for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

SMILES for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

INCHI for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

Structure for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)

3D Structure for NP0092351 (rac-4-Hydroxy-4-O-(beta-D-glucuronide)-all-trans-retinyl acetate)