NP-MRD: Showing NP-Card for 5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one (NP0222875)

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Record Information

Version

2.0

Created at

2022-09-06 00:49:06 UTC

Updated at

2022-09-06 00:49:06 UTC

NP-MRD ID

NP0222875

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one

Description

5-Hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]Undecan-2-one 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-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one is found in Verbena brasiliensis. 5-Hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]Undecan-2-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004151519302D          

 26 29  0  0  0  0            999 V2000
    0.6213   -1.4832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0605   -0.7849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420   -0.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0609    0.1658    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3673    0.5143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5569    1.3172    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3792    1.3849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8076    2.0900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6977    0.6239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4764    0.3514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1017    0.8895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8804    0.6170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5058    1.1551    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2845    0.8826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9098    1.4208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7565    2.2314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4378    0.0720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2165   -0.2005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8125   -0.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9658   -1.2767    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0338   -0.1936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4084   -0.7317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6297   -0.4592    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0044   -0.9973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2257   -0.7248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0724    0.0858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  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
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 12 21  1  0  0  0  0
 21 22  1  0  0  0  0
 10 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
  2 25  1  0  0  0  0
 25 26  1  0  0  0  0
  5 26  1  0  0  0  0
  9 26  1  0  0  0  0
M  END


  Mrv1533004151519302D          

 26 29  0  0  0  0            999 V2000
    0.6213   -1.4832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0605   -0.7849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420   -0.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0609    0.1658    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3673    0.5143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5569    1.3172    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3792    1.3849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8076    2.0900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6977    0.6239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4764    0.3514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1017    0.8895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8804    0.6170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5058    1.1551    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2845    0.8826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9098    1.4208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7565    2.2314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4378    0.0720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2165   -0.2005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8125   -0.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9658   -1.2767    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0338   -0.1936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4084   -0.7317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6297   -0.4592    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0044   -0.9973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2257   -0.7248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0724    0.0858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  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
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 12 21  1  0  0  0  0
 21 22  1  0  0  0  0
 10 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
  2 25  1  0  0  0  0
 25 26  1  0  0  0  0
  5 26  1  0  0  0  0
  9 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0222875

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1C(O)C2OC(=O)C3C2C1COC3OC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C16H24O10/c1-4-5-3-23-15(8-7(5)13(9(4)18)25-14(8)22)26-16-12(21)11(20)10(19)6(2-17)24-16/h4-13,15-21H,2-3H2,1H3

> <INCHI_KEY>
VFBJKEKWRZAYGB-UHFFFAOYSA-N

> <FORMULA>
C16H24O10

> <MOLECULAR_WEIGHT>
376.358

> <EXACT_MASS>
376.136946973

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
36.1310456042723

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one

> <ALOGPS_LOGP>
-1.91

> <JCHEM_LOGP>
-2.5028818153333328

> <ALOGPS_LOGS>
-0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.130950175177748

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.198623934547083

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981084760132018

> <JCHEM_POLAR_SURFACE_AREA>
155.14000000000001

> <JCHEM_REFRACTIVITY>
80.43600000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.44e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         0                                  
HETATM    1  C   UNK     0       1.160  -2.769   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.980  -1.465   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.385  -0.045   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.114   0.309   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.552   0.960   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.906   2.459   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.441   2.585   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.241   3.901   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.036   1.165   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.489   0.656   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       7.657   1.660   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       9.110   1.152   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      10.277   2.156   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      11.731   1.648   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.898   2.652   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.612   4.165   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      12.017   0.134   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      13.471  -0.374   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.850  -0.870   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      11.136  -2.383   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.396  -0.361   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.229  -1.366   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.776  -0.857   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       5.608  -1.862   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.155  -1.353   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.868   0.160   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   25                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   26                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   26                                                  
CONECT   10    9   11   23                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   12   22                                                  
CONECT   22   21                                                            
CONECT   23   10   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24    2   26                                                  
CONECT   26   25    5    9                                                  
MASTER        0    0    0    0    0    0    0    0   26    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₂₄O₁₀

Average Mass

376.3580 Da

Monoisotopic Mass

376.13695 Da

IUPAC Name

5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one

Traditional Name

5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one

CAS Registry Number

Not Available

SMILES

CC1C(O)C2OC(=O)C3C2C1COC3OC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C16H24O10/c1-4-5-3-23-15(8-7(5)13(9(4)18)25-14(8)22)26-16-12(21)11(20)10(19)6(2-17)24-16/h4-13,15-21H,2-3H2,1H3

InChI Key

VFBJKEKWRZAYGB-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Verbena brasiliensis	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
Furopyran
Gamma butyrolactone
Monosaccharide
Oxane
Pyran
Cyclic alcohol
Furan
Tetrahydrofuran
Lactone
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Acetal
Carboxylic acid derivative
Polyol
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Primary 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	-1.9	ALOGPS
logP	-2.5	ChemAxon
logS	-0.19	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	155.14 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	80.44 m³·mol⁻¹	ChemAxon
Polarizability	36.13 Å³	ChemAxon
Number of Rings	4	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

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

74934495

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one (NP0222875)

MOL for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

3D MOL for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

3D SDF for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

3D-SDF for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

PDB for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

3D PDB for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

SMILES for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

INCHI for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

Structure for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)

3D Structure for NP0222875 (5-hydroxy-6-methyl-10-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undecan-2-one)