NP-MRD: Showing NP-Card for (1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol (NP0164865)

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Record Information

Version

2.0

Created at

2022-09-02 23:49:49 UTC

Updated at

2022-09-02 23:49:50 UTC

NP-MRD ID

NP0164865

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol

Description

Jioglutin D belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms. (1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol is found in Rehmannia glutinosa. Based on a literature review very few articles have been published on Jioglutin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309032201492D          

 17 19  0  0  1  0            999 V2000
   -1.4655    0.3033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8697    0.8739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0776    0.6432    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5182    1.2138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3103    0.9831    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0118    1.4174    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0727    2.2401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6415    0.8845    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1467    0.2322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3293    0.1208    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3547   -0.7038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0815   -1.0941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5066    0.1818    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9107   -0.3888    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1070   -1.1901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5111   -1.7608    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1186   -0.1581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 13 10  1  1  0  0  0
  5 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
  3 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0164865

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]1C[C@H]2[C@H](O)[C@@H]3O[C@]3(CO)[C@H]2[C@@H](OC)O1

> <INCHI_IDENTIFIER>
InChI=1S/C11H18O6/c1-14-6-3-5-7(10(15-2)16-6)11(4-12)9(17-11)8(5)13/h5-10,12-13H,3-4H2,1-2H3/t5-,6+,7-,8+,9+,10+,11-/m1/s1

> <INCHI_KEY>
BVYJKUKAFKCKMT-GYQMHZIISA-N

> <FORMULA>
C11H18O6

> <MOLECULAR_WEIGHT>
246.259

> <EXACT_MASS>
246.1103383

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
24.38808991132801

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,4S,5S,6R,8S,10S)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-5-ol

> <ALOGPS_LOGP>
-0.85

> <JCHEM_LOGP>
-0.9796194093333331

> <ALOGPS_LOGS>
-0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.403955508317548

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.689109876832578

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1215449389350374

> <JCHEM_POLAR_SURFACE_AREA>
80.68

> <JCHEM_REFRACTIVITY>
55.3278

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.94e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4S,5S,6R,8S,10S)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-5-ol

> <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      -2.736   0.566   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.623   1.631   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.145   1.201   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.967   2.266   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.446   1.835   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.755   2.646   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.869   4.182   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.931   1.651   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.874   0.433   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.348   0.226   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.395  -1.314   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.752  -2.042   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.812   0.339   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.700  -0.726   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.066  -2.222   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.954  -3.287   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.221  -0.295   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8   10                                                       
CONECT   10    9    8   11   13                                             
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10    5   14                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14    3                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₈O₆

Average Mass

246.2590 Da

Monoisotopic Mass

246.11034 Da

IUPAC Name

(1S,2S,4S,5S,6R,8S,10S)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-5-ol

Traditional Name

(1S,2S,4S,5S,6R,8S,10S)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-5-ol

CAS Registry Number

Not Available

SMILES

CO[C@@H]1C[C@H]2[C@H](O)[C@@H]3O[C@]3(CO)[C@H]2[C@@H](OC)O1

InChI Identifier

InChI=1S/C11H18O6/c1-14-6-3-5-7(10(15-2)16-6)11(4-12)9(17-11)8(5)13/h5-10,12-13H,3-4H2,1-2H3/t5-,6+,7-,8+,9+,10+,11-/m1/s1

InChI Key

BVYJKUKAFKCKMT-GYQMHZIISA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Rehmannia glutinosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxanes

Sub Class

Not Available

Direct Parent

Oxanes

Alternative Parents

Substituents

Oxane
Cyclic alcohol
Secondary alcohol
Oxacycle
Ether
Oxirane
Dialkyl ether
Acetal
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
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	-0.85	ALOGPS
logP	-0.98	ChemAxon
logS	-0.1	ALOGPS
pKa (Strongest Acidic)	13.69	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	80.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	55.33 m³·mol⁻¹	ChemAxon
Polarizability	24.39 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	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00051035

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

14486934

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol (NP0164865)

MOL for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

3D MOL for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

3D SDF for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

3D-SDF for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

PDB for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

3D PDB for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

SMILES for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

INCHI for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

Structure for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)

3D Structure for NP0164865 ((1s,2s,4s,5s,6r,8s,10s)-2-(hydroxymethyl)-8,10-dimethoxy-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-5-ol)