NP-MRD: Showing NP-Card for Columbin (NP0052001)

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Record Information

Version

2.0

Created at

2022-04-27 23:11:48 UTC

Updated at

2022-04-27 23:11:48 UTC

NP-MRD ID

NP0052001

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Columbin

Description

(1S,2S,3S,5R,8R,11R,12R)-5-(furan-3-yl)-12-hydroxy-3,11-dimethyl-6,14-dioxatetracyclo[10.2.2.0²,¹¹.0³,⁸]Hexadec-15-ene-7,13-dione belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings. Columbin is found in Calystegia hedracea, Cleidion spiciflorum (Burm. f.) Merr. , Dioscoreophyllum cummingsii, Dioscoreophyllum cumminsii, Jateorhiza palmata , Tinospora sagittata , Solanum dulcamara , Solanum lyratum , Tinospora capillipes, Tinospora crispa and Tinospora dentata. Based on a literature review very few articles have been published on (1S,2S,3S,5R,8R,11R,12R)-5-(furan-3-yl)-12-hydroxy-3,11-dimethyl-6,14-dioxatetracyclo[10.2.2.0²,¹¹.0³,⁸]Hexadec-15-ene-7,13-dione.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282201112D          

 26 30  0  0  1  0            999 V2000
    1.1119   -0.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8621    0.4781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7348    1.0305    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5586    0.9875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9334    0.2525    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4842   -0.4395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6603   -0.3965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2856    0.3385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5383    0.3815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7572    0.2096    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2064    0.9016    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8317    1.6366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0078    1.6795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0303    0.8586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4795    1.5506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4050    0.1236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9558   -0.5684    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1319   -0.5254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3305   -1.3034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1454   -1.4323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2746   -2.2471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5396   -2.6218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9561   -2.0386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3081   -0.4825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1839    1.7225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3601    1.7655    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  6  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
  4 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 10 18  1  0  0  0  0
 17 19  1  1  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 19 23  1  0  0  0  0
 10 24  1  6  0  0  0
  4 25  1  1  0  0  0
  3 26  1  1  0  0  0
M  END


  Mrv1652304282201112D          

 26 30  0  0  1  0            999 V2000
    1.1119   -0.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8621    0.4781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7348    1.0305    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5586    0.9875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9334    0.2525    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4842   -0.4395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6603   -0.3965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2856    0.3385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5383    0.3815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7572    0.2096    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2064    0.9016    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8317    1.6366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0078    1.6795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0303    0.8586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4795    1.5506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4050    0.1236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9558   -0.5684    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1319   -0.5254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3305   -1.3034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1454   -1.4323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2746   -2.2471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5396   -2.6218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9561   -2.0386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3081   -0.4825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1839    1.7225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3601    1.7655    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  6  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
  4 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 10 18  1  0  0  0  0
 17 19  1  1  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 19 23  1  0  0  0  0
 10 24  1  6  0  0  0
  4 25  1  1  0  0  0
  3 26  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0052001

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@]12C[C@@H](OC(=O)[C@@H]1CC[C@]1(C)[C@H]2[C@H]2OC(=O)[C@@]1(O)C=C2)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H22O6/c1-18-9-14(11-5-8-24-10-11)25-16(21)12(18)3-6-19(2)15(18)13-4-7-20(19,23)17(22)26-13/h4-5,7-8,10,12-15,23H,3,6,9H2,1-2H3/t12-,13-,14+,15-,18+,19+,20-/m0/s1

> <INCHI_KEY>
AALLCALQGXXWNA-NXLUFJALSA-N

> <FORMULA>
C20H22O6

> <MOLECULAR_WEIGHT>
358.39

> <EXACT_MASS>
358.141638428

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
40.221989562868565

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,3S,5R,8R,11R,12R)-5-(furan-3-yl)-12-hydroxy-3,11-dimethyl-6,14-dioxatetracyclo[10.2.2.0^{2,11}.0^{3,8}]hexadec-15-ene-7,13-dione

> <ALOGPS_LOGP>
2.04

> <JCHEM_LOGP>
2.154485321666666

> <ALOGPS_LOGS>
-3.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.624383809380962

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8885975695530357

> <JCHEM_POLAR_SURFACE_AREA>
85.97000000000001

> <JCHEM_REFRACTIVITY>
90.22420000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.40e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,3S,5R,8R,11R,12R)-5-(furan-3-yl)-12-hydroxy-3,11-dimethyl-6,14-dioxatetracyclo[10.2.2.0^{2,11}.0^{3,8}]hexadec-15-ene-7,13-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       2.076  -0.022   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.609   0.892   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.372   1.924   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.909   1.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.609   0.471   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.770  -0.820   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.233  -0.740   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.533   0.632   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.005   0.712   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       5.147   0.391   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.985   1.683   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.286   3.055   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.748   3.135   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.523   1.603   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.362   2.894   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       8.223   0.231   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       7.384  -1.061   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.846  -0.981   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.084  -2.433   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.605  -2.674   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.846  -4.195   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       8.474  -4.894   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.385  -3.805   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.308  -0.901   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.210   3.215   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.672   3.296   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8   26                                             
CONECT    4    3    5   13   25                                             
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    3    9                                                  
CONECT    9    8                                                            
CONECT   10    5   11   18   24                                             
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12    4                                                       
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17   10                                                       
CONECT   19   17   20   23                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   19                                                       
CONECT   24   10                                                            
CONECT   25    4                                                            
CONECT   26    3                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₂O₆

Average Mass

358.3900 Da

Monoisotopic Mass

358.14164 Da

IUPAC Name

(1S,2S,3S,5R,8R,11R,12R)-5-(furan-3-yl)-12-hydroxy-3,11-dimethyl-6,14-dioxatetracyclo[10.2.2.0^{2,11}.0^{3,8}]hexadec-15-ene-7,13-dione

Traditional Name

(1S,2S,3S,5R,8R,11R,12R)-5-(furan-3-yl)-12-hydroxy-3,11-dimethyl-6,14-dioxatetracyclo[10.2.2.0^{2,11}.0^{3,8}]hexadec-15-ene-7,13-dione

CAS Registry Number

Not Available

SMILES

C[C@@]12C[C@@H](OC(=O)[C@@H]1CC[C@]1(C)[C@H]2[C@H]2OC(=O)[C@@]1(O)C=C2)C1=COC=C1

InChI Identifier

InChI=1S/C20H22O6/c1-18-9-14(11-5-8-24-10-11)25-16(21)12(18)3-6-19(2)15(18)13-4-7-20(19,23)17(22)26-13/h4-5,7-8,10,12-15,23H,3,6,9H2,1-2H3/t12-,13-,14+,15-,18+,19+,20-/m0/s1

InChI Key

AALLCALQGXXWNA-NXLUFJALSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Calystegia hedracea	Plant	KNApSAcK
Cleidion spiciflorum (Burm. f.) Merr.	Plant	KNApSAcK
Dioscoreophyllum cummingsii	Plant	KNApSAcK
Dioscoreophyllum cumminsii	Plant	KNApSAcK
Jateorhiza palmata	Plant	KNApSAcK
Paratinospora sagittata	Plant	KNApSAcK
Solanum dulcamara	Plant	KNApSAcK
Solanum lyratum	Plant	KNApSAcK
Tinospora capillipes	Plant	KNApSAcK
Tinospora crispa	Plant	KNApSAcK
Tinospora dentata	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthopyrans

Sub Class

Not Available

Direct Parent

Naphthopyrans

Alternative Parents

Substituents

Naphthopyran
Naphthalene
Delta valerolactone
Dihydropyranone
Delta_valerolactone
Pyran
Oxane
Dicarboxylic acid or derivatives
Tertiary alcohol
Heteroaromatic compound
Furan
Carboxylic acid ester
Lactone
Carboxylic acid derivative
Oxacycle
Organic oxygen compound
Organic oxide
Alcohol
Hydrocarbon derivative
Carbonyl group
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	2.04	ALOGPS
logP	2.15	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	11.62	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	85.97 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	90.22 m³·mol⁻¹	ChemAxon
Polarizability	40.22 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

71481131

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Columbin (NP0052001)

MOL for NP0052001 (Columbin)

3D MOL for NP0052001 (Columbin)

3D SDF for NP0052001 (Columbin)

3D-SDF for NP0052001 (Columbin)

PDB for NP0052001 (Columbin)

3D PDB for NP0052001 (Columbin)

SMILES for NP0052001 (Columbin)

INCHI for NP0052001 (Columbin)

Structure for NP0052001 (Columbin)

3D Structure for NP0052001 (Columbin)