NP-MRD: Showing NP-Card for 5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol (NP0173379)

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Record Information

Version

2.0

Created at

2022-09-03 10:30:17 UTC

Updated at

2022-09-03 10:30:17 UTC

NP-MRD ID

NP0173379

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol

Description

5-(Hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. 5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol is found in Nuxia floribunda. Based on a literature review very few articles have been published on 5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032212302D          

 34 38  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309032212302D          

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M  END
> <DATABASE_ID>
NP0173379

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OC(OC2C3OC3C3C2C=COC3OC2C(O)C(O)C(O)C(O)C2CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H32O13/c1-5-9(23)11(25)15(29)21(31-5)34-17-6-2-3-30-20(8(6)18-19(17)32-18)33-16-7(4-22)10(24)12(26)13(27)14(16)28/h2-3,5-29H,4H2,1H3

> <INCHI_KEY>
IZUBISXPQXRBMI-UHFFFAOYSA-N

> <FORMULA>
C21H32O13

> <MOLECULAR_WEIGHT>
492.474

> <EXACT_MASS>
492.18429109

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
47.4328090893848

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol

> <ALOGPS_LOGP>
-2.03

> <JCHEM_LOGP>
-4.244847649666667

> <ALOGPS_LOGS>
-0.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.644543073117298

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.07015756185885

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6684065343986516

> <JCHEM_POLAR_SURFACE_AREA>
211.29

> <JCHEM_REFRACTIVITY>
106.61800000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       2.085   5.907   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.199   4.371   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.586   3.702   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       3.700   2.166   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.087   1.497   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.200  -0.039   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.510  -0.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.988  -0.419   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.101  -1.484   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.734  -2.980   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.256  -3.411   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.889  -4.906   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.002  -5.971   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.480  -5.541   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       9.846  -4.045   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      10.592  -6.606   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      12.071  -6.175   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.226  -8.102   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.338  -9.167   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.747  -8.532   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       8.381 -10.028   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       7.635  -7.467   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.157  -7.898   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.044  -6.833   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.143  -2.345   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.608  -2.459   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       3.082  -2.251   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       4.025  -1.034   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.426   1.300   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.540  -0.236   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.040   1.969   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -0.234   1.103   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.926   3.505   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -0.461   4.174   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   29                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   28                                                  
CONECT    7    6    8   25                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   25                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   22                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   13   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   11    7   26                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26   28                                                       
CONECT   28   27    6   26                                                  
CONECT   29    4   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31    2   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₂O₁₃

Average Mass

492.4740 Da

Monoisotopic Mass

492.18429 Da

IUPAC Name

5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol

Traditional Name

5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol

CAS Registry Number

Not Available

SMILES

CC1OC(OC2C3OC3C3C2C=COC3OC2C(O)C(O)C(O)C(O)C2CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C21H32O13/c1-5-9(23)11(25)15(29)21(31-5)34-17-6-2-3-30-20(8(6)18-19(17)32-18)33-16-7(4-22)10(24)12(26)13(27)14(16)28/h2-3,5-29H,4H2,1H3

InChI Key

IZUBISXPQXRBMI-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
Nuxia floribunda	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Hexose monosaccharide
O-glycosyl compound
Cyclohexanol
Cyclitol or derivatives
Monosaccharide
Oxane
Cyclic alcohol
Secondary alcohol
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Oxacycle
Acetal
Polyol
Primary alcohol
Hydrocarbon derivative
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	-2	ALOGPS
logP	-4.2	ChemAxon
logS	-0.68	ALOGPS
pKa (Strongest Acidic)	12.07	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	211.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	106.62 m³·mol⁻¹	ChemAxon
Polarizability	47.43 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

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

162904494

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol (NP0173379)

MOL for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

3D MOL for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

3D SDF for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

3D-SDF for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

PDB for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

3D PDB for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

SMILES for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

INCHI for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

Structure for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)

3D Structure for NP0173379 (5-(hydroxymethyl)-6-({5-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-10-yl}oxy)cyclohexane-1,2,3,4-tetrol)