NP-MRD: Showing NP-Card for (1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol (NP0265830)

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Record Information

Version

2.0

Created at

2022-09-08 09:57:40 UTC

Updated at

2022-09-08 09:57:40 UTC

NP-MRD ID

NP0265830

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol

Description

Dambonitol belongs to the class of organic compounds known as cyclohexanols. Cyclohexanols are compounds containing an alcohol group attached to a cyclohexane ring. (1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol is found in Dyera costulata and Strophanthus divaricatus. (1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol was first documented in 2022 (PMID: 35052998). Based on a literature review very few articles have been published on Dambonitol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 30  0  0  0  0  0  0  0  0999 V2000
    3.0111   -1.5549   -0.6416 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7710   -1.0457   -0.9717 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2086   -0.2718    0.0433 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0728   -0.8206    0.4912 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0998   -2.2073    0.2012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3194   -0.2367   -0.0646 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8117   -1.0064   -1.1201 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0748   -1.4997   -0.8750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1988    1.1685   -0.5695 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3721    1.8709   -0.3793 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0351    1.8157    0.1669 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0046    3.1517   -0.1942 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1905    1.1523   -0.4423 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2988    1.8822   -0.0297 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8981   -2.1896    0.2547 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6787   -0.6980   -0.3722 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3853   -2.1221   -1.4995 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9645   -0.2837    0.8847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1209   -0.7767    1.6107 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4907   -2.7133    0.8094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1164   -0.2363    0.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4036   -2.0922   -1.7365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7499   -0.6086   -0.7294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1284   -2.0907    0.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9494    1.1287   -1.6498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1930    2.8230   -0.5344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1080    1.6362    1.2417 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0875    3.1893   -1.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0885    1.1826   -1.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6762    1.4535    0.7700 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3 13  1  0
 13 14  1  0
 13 11  1  0
 11 12  1  0
 11  9  1  0
  9 10  1  0
  9  6  1  0
  6  7  1  0
  7  8  1  0
  6  4  1  0
  4  5  1  0
  4  3  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  1
 13 29  1  6
 14 30  1  0
 11 27  1  1
 12 28  1  0
  9 25  1  6
 10 26  1  0
  6 21  1  1
  8 22  1  0
  8 23  1  0
  8 24  1  0
  4 19  1  1
  5 20  1  0
M  END


  Mrv1652309082211572D          

 14 14  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    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
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
  3 13  1  0  0  0  0
 13 14  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0265830

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@H]1[C@H](O)C(O)[C@H](O)[C@@H](OC)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H16O6/c1-13-7-4(10)3(9)5(11)8(14-2)6(7)12/h3-12H,1-2H3/t3?,4-,5+,6?,7+,8-

> <INCHI_KEY>
MMCIFJWGSIWJLP-XAMPRYAMSA-N

> <FORMULA>
C8H16O6

> <MOLECULAR_WEIGHT>
208.21

> <EXACT_MASS>
208.094688235

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
20.13739673143771

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3S,4R,6S)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol

> <JCHEM_LOGP>
-2.4957566446666677

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.090514629373626

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.45236766699266

> <JCHEM_PKA_STRONGEST_BASIC>
-3.646177517028888

> <JCHEM_POLAR_SURFACE_AREA>
99.38000000000001

> <JCHEM_REFRACTIVITY>
45.27739999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,4R,6S)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   13                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    3   14                                                  
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₈H₁₆O₆

Average Mass

208.2100 Da

Monoisotopic Mass

208.09469 Da

IUPAC Name

(1R,3S,4R,6S)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol

Traditional Name

(1R,3S,4R,6S)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol

CAS Registry Number

Not Available

SMILES

CO[C@H]1[C@H](O)C(O)[C@H](O)[C@@H](OC)C1O

InChI Identifier

InChI=1S/C8H16O6/c1-13-7-4(10)3(9)5(11)8(14-2)6(7)12/h3-12H,1-2H3/t3?,4-,5+,6?,7+,8-

InChI Key

MMCIFJWGSIWJLP-XAMPRYAMSA-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
Dyera costulata	LOTUS Database	35616633
Strophanthus divaricatus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclohexanols. Cyclohexanols are compounds containing an alcohol group attached to a cyclohexane ring.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Cyclohexanols

Alternative Parents

Substituents

Cyclohexanol
Cyclitol or derivatives
Cyclic alcohol
Polyol
Ether
Dialkyl ether
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	-2.5	ChemAxon
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	99.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	45.28 m³·mol⁻¹	ChemAxon
Polarizability	20.14 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

75699662

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21627888

PDB ID

Not Available

ChEBI ID

173588

Good Scents ID

Not Available

References

General References

Ngah L, Tsopgni WDT, Nyobe JCN, Tcho AT, Langat MK, Ndom JC, Mas-Claret E, Sadgrove NJ, Waffo AFK, Phumthum M: A New Antimicrobial Phenylpropanol from the Leaves of Tabernaemontana inconspicua Stapf. (Apocynaceae) Inhibits Pathogenic Gram-Negative Bacteria. Antibiotics (Basel). 2022 Jan 17;11(1). pii: antibiotics11010121. doi: 10.3390/antibiotics11010121. [PubMed:35052998 ]
LOTUS database [Link]

Showing NP-Card for (1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol (NP0265830)

MOL for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

3D MOL for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

3D SDF for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

3D-SDF for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

PDB for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

3D PDB for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

SMILES for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

INCHI for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

Structure for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)

3D Structure for NP0265830 ((1r,3s,4r,6s)-4,6-dimethoxycyclohexane-1,2,3,5-tetrol)