NP-MRD: Showing NP-Card for β-d-glucosyl crocetin (NP0295526)

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Record Information

Version

2.0

Created at

2022-09-10 04:32:46 UTC

Updated at

2022-09-10 04:32:47 UTC

NP-MRD ID

NP0295526

Secondary Accession Numbers

None

Natural Product Identification

Common Name

β-d-glucosyl crocetin

Description

Beta-D-glucosyl crocetin, also known as crocetin b-D-glucosyl ester, belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. β-d-glucosyl crocetin is found in Crocus sativus and Gardenia jasminoides. β-d-glucosyl crocetin was first documented in 2020 (PMID: 32127777). Based on a literature review very few articles have been published on beta-D-glucosyl crocetin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102206322D          

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M  END

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M  END
> <DATABASE_ID>
NP0295526

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C26H34O9/c1-16(11-7-13-18(3)24(31)32)9-5-6-10-17(2)12-8-14-19(4)25(33)35-26-23(30)22(29)21(28)20(15-27)34-26/h5-14,20-23,26-30H,15H2,1-4H3,(H,31,32)/b6-5+,11-7+,12-8+,16-9+,17-10+,18-13+,19-14+/t20-,21-,22+,23-,26+/m1/s1

> <INCHI_KEY>
ZVGODNZUEWDIPM-YXRLTKITSA-N

> <FORMULA>
C26H34O9

> <MOLECULAR_WEIGHT>
490.549

> <EXACT_MASS>
490.220282675

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.00097873735707

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E,4E,6E,8E,10E,12E,14E)-2,6,11,15-tetramethyl-16-oxo-16-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hexadeca-2,4,6,8,10,12,14-heptaenoic acid

> <JCHEM_LOGP>
2.365468470666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.195723025639856

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.9462094497688875

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810938228983064

> <JCHEM_POLAR_SURFACE_AREA>
153.75

> <JCHEM_REFRACTIVITY>
136.22800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
β-D-glucosyl crocetin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       8.002  15.400   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  16.170   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  17.710   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002  18.480   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002  20.020   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.336  20.790   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.669  20.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336  22.330   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      10.669  23.100   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.002  23.100   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.335  15.400   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  13.860   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    2   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   34                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   27   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   25   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   70    0
END

View in JSmol

Synonyms

Value	Source
all-trans-Crocetin mono(beta-D-glucosyl) ester	ChEBI
Crocetin beta-D-glucopyranosyl ester	ChEBI
Crocetin beta-D-glucosyl ester	ChEBI
Crocetin mono(beta-D-glucosyl) ester	ChEBI
trans-Crocetin beta-D-glucosyl ester	ChEBI
all-trans-Crocetin mono(b-D-glucosyl) ester	Generator
all-trans-Crocetin mono(β-D-glucosyl) ester	Generator
Crocetin b-D-glucopyranosyl ester	Generator
Crocetin β-D-glucopyranosyl ester	Generator
Crocetin b-D-glucosyl ester	Generator
Crocetin β-D-glucosyl ester	Generator
Crocetin mono(b-D-glucosyl) ester	Generator
Crocetin mono(β-D-glucosyl) ester	Generator
trans-Crocetin b-D-glucosyl ester	Generator
trans-Crocetin β-D-glucosyl ester	Generator
b-D-Glucosyl crocetin	Generator
Β-D-glucosyl crocetin	Generator

Chemical Formula

C₂₆H₃₄O₉

Average Mass

490.5490 Da

Monoisotopic Mass

490.22028 Da

IUPAC Name

(2E,4E,6E,8E,10E,12E,14E)-2,6,11,15-tetramethyl-16-oxo-16-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}hexadeca-2,4,6,8,10,12,14-heptaenoic acid

Traditional Name

β-D-glucosyl crocetin

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C26H34O9/c1-16(11-7-13-18(3)24(31)32)9-5-6-10-17(2)12-8-14-19(4)25(33)35-26-23(30)22(29)21(28)20(15-27)34-26/h5-14,20-23,26-30H,15H2,1-4H3,(H,31,32)/b6-5+,11-7+,12-8+,16-9+,17-10+,18-13+,19-14+/t20-,21-,22+,23-,26+/m1/s1

InChI Key

ZVGODNZUEWDIPM-YXRLTKITSA-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
Crocus sativus	LOTUS Database	35616633
Gardenia jasminoides	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Saccharolipid
Long-chain fatty acid
Hexose monosaccharide
Branched fatty acid
Fatty acid ester
Heterocyclic fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Sugar acid
Dicarboxylic acid or derivatives
Fatty acyl
Unsaturated fatty acid
Monosaccharide
Oxane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Carboxylic acid ester
Acetal
Organoheterocyclic compound
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Polyol
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

dicarboxylic acid monoester (CHEBI:62765 )
beta-D-glucoside (CHEBI:62765 )

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	2.37	ChemAxon
pKa (Strongest Acidic)	4.95	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	153.75 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	136.23 m³·mol⁻¹	ChemAxon
Polarizability	53 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

8543747

KEGG Compound ID

C19867

BioCyc ID

CPD-8663

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10368299

PDB ID

Not Available

ChEBI ID

62765

Good Scents ID

Not Available

References

General References

Mir MA, Ganai SA, Mansoor S, Jan S, Mani P, Masoodi KZ, Amin H, Rehman MU, Ahmad P: Isolation, purification and characterization of naturally derived Crocetin beta-d-glucosyl ester from Crocus sativus L. against breast cancer and its binding chemistry with ER-alpha/HDAC2. Saudi J Biol Sci. 2020 Mar;27(3):975-984. doi: 10.1016/j.sjbs.2020.01.018. Epub 2020 Jan 27. [PubMed:32127777 ]
LOTUS database [Link]

Showing NP-Card for β-d-glucosyl crocetin (NP0295526)

MOL for NP0295526 (β-d-glucosyl crocetin)

3D MOL for NP0295526 (β-d-glucosyl crocetin)

3D SDF for NP0295526 (β-d-glucosyl crocetin)

3D-SDF for NP0295526 (β-d-glucosyl crocetin)

PDB for NP0295526 (β-d-glucosyl crocetin)

3D PDB for NP0295526 (β-d-glucosyl crocetin)

SMILES for NP0295526 (β-d-glucosyl crocetin)

INCHI for NP0295526 (β-d-glucosyl crocetin)

Structure for NP0295526 (β-d-glucosyl crocetin)

3D Structure for NP0295526 (β-d-glucosyl crocetin)