NP-MRD: Showing NP-Card for Phytuberin (NP0048312)

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Record Information

Version

2.0

Created at

2022-03-17 20:54:27 UTC

Updated at

2022-03-17 20:54:28 UTC

NP-MRD ID

NP0048312

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phytuberin

Description

Phytuberin belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Phytuberin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, phytuberin has been detected, but not quantified in, potato. Phytuberin is found in Erwinia carotovora, Nicotiana glutinosa, Nicotiana rustica, Nicotiana tabacum , Nicotiana undulata and Solanum lycopersicum. This could make phytuberin a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061308422D          

 21 23  0  0  0  0            999 V2000
    2.9046    4.8606    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4105    2.8551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0314    2.5466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3233   -0.3317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7225   -0.0471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6915    1.3516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5372    0.5411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8032    0.9194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1226    1.6801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2877    1.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4389   -0.4912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7504    4.0501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667    1.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2209    2.7009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7582    0.2695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4280    0.3806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1335    0.8083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9714    3.7784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9447    1.6114    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6167   -0.4225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3752    3.5113    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0  0  0  0
  9  8  2  0  0  0  0
 12  1  1  0  0  0  0
 13  6  1  0  0  0  0
 13 10  1  0  0  0  0
 14  2  1  0  0  0  0
 14  3  1  0  0  0  0
 14 13  1  0  0  0  0
 15  4  1  0  0  0  0
 15  7  1  0  0  0  0
 15 11  1  0  0  0  0
 16  5  1  0  0  0  0
 16  8  1  0  0  0  0
 17 10  1  0  0  0  0
 17 15  1  0  0  0  0
 17 16  1  0  0  0  0
 18 12  2  0  0  0  0
 19  9  1  0  0  0  0
 19 17  1  0  0  0  0
 20 11  1  0  0  0  0
 20 16  1  0  0  0  0
 21 12  1  0  0  0  0
 21 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048312

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)OC(C)(C)C1CCC2(C)COC3(C)C=COC23C1

> <INCHI_IDENTIFIER>
InChI=1S/C17H26O4/c1-12(18)21-14(2,3)13-6-7-15(4)11-20-16(5)8-9-19-17(15,16)10-13/h8-9,13H,6-7,10-11H2,1-5H3

> <INCHI_KEY>
YARAJYKHRCCDLG-UHFFFAOYSA-N

> <FORMULA>
C17H26O4

> <MOLECULAR_WEIGHT>
294.3859

> <EXACT_MASS>
294.18310932

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
32.16241056270249

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{5,8-dimethyl-2,6-dioxatricyclo[6.4.0.0¹,⁵]dodec-3-en-11-yl}propan-2-yl acetate

> <ALOGPS_LOGP>
3.66

> <JCHEM_LOGP>
2.317423118333332

> <ALOGPS_LOGS>
-4.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.11312517597911

> <JCHEM_POLAR_SURFACE_AREA>
44.760000000000005

> <JCHEM_REFRACTIVITY>
79.1392

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.24e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{5,8-dimethyl-2,6-dioxatricyclo[6.4.0.0¹,⁵]dodec-3-en-11-yl}propan-2-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       5.422   9.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.500   5.330   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.525   4.754   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.203  -0.619   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.349  -0.088   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.891   2.523   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.603   1.010   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.499   1.716   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.096   3.136   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.270   3.022   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.553  -0.917   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.134   7.560   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.725   3.529   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.012   5.042   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.149   0.503   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.666   0.710   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.983   1.509   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.680   7.053   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.630   3.008   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       3.018  -0.789   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.300   6.554   0.000  0.00  0.00           O+0
CONECT    1   12                                                            
CONECT    2   14                                                            
CONECT    3   14                                                            
CONECT    4   15                                                            
CONECT    5   16                                                            
CONECT    6    7   13                                                       
CONECT    7    6   15                                                       
CONECT    8    9   16                                                       
CONECT    9    8   19                                                       
CONECT   10   13   17                                                       
CONECT   11   15   20                                                       
CONECT   12    1   18   21                                                  
CONECT   13    6   10   14                                                  
CONECT   14    2    3   13   21                                             
CONECT   15    4    7   11   17                                             
CONECT   16    5    8   17   20                                             
CONECT   17   10   15   16   19                                             
CONECT   18   12                                                            
CONECT   19    9   17                                                       
CONECT   20   11   16                                                       
CONECT   21   12   14                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
(-)-Phytuberin	HMDB
(3AR,5as,8R,9ar)-5,5a,6,7,8,9-hexahydro-a,a,3a,5a-tetramethyl-3ah-furo[3,2-c]isobenzofuran-8-methanol acetate	HMDB
2-{5,8-dimethyl-2,6-dioxatricyclo[6.4.0.0¹,⁵]dodec-3-en-11-yl}propan-2-yl acetic acid	Generator
Phytuberin	MeSH

Chemical Formula

C₁₇H₂₆O₄

Average Mass

294.3859 Da

Monoisotopic Mass

294.18311 Da

IUPAC Name

2-{5,8-dimethyl-2,6-dioxatricyclo[6.4.0.0¹,⁵]dodec-3-en-11-yl}propan-2-yl acetate

Traditional Name

2-{5,8-dimethyl-2,6-dioxatricyclo[6.4.0.0¹,⁵]dodec-3-en-11-yl}propan-2-yl acetate

CAS Registry Number

37209-50-0

SMILES

CC(=O)OC(C)(C)C1CCC2(C)COC3(C)C=COC23C1

InChI Identifier

InChI=1S/C17H26O4/c1-12(18)21-14(2,3)13-6-7-15(4)11-20-16(5)8-9-19-17(15,16)10-13/h8-9,13H,6-7,10-11H2,1-5H3

InChI Key

YARAJYKHRCCDLG-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Erwinia carotovora	Bacteria	KNApSAcK
Nicotiana glutinosa	LOTUS Database	35616633
Nicotiana rustica	LOTUS Database	35616633
Nicotiana tabacum	Plant	KNApSAcK
Nicotiana undulata	LOTUS Database	35616633
Solanum lycopersicum	LOTUS Database	35616633
Solanum tuberosum	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Sesquiterpenoid
Furofuran
Dihydrofuran
Tetrahydrofuran
Carboxylic acid ester
Carboxylic acid derivative
Dialkyl ether
Ether
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Carbonyl group
Organic oxide
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	3.66	ALOGPS
logP	2.32	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	44.76 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	79.14 m³·mol⁻¹	ChemAxon
Polarizability	32.16 Å³	ChemAxon
Number of Rings	3	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

HMDB0035754

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

315114

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Phytuberin (NP0048312)

MOL for NP0048312 (Phytuberin)

3D MOL for NP0048312 (Phytuberin)

3D SDF for NP0048312 (Phytuberin)

3D-SDF for NP0048312 (Phytuberin)

PDB for NP0048312 (Phytuberin)

3D PDB for NP0048312 (Phytuberin)

SMILES for NP0048312 (Phytuberin)

INCHI for NP0048312 (Phytuberin)

Structure for NP0048312 (Phytuberin)

3D Structure for NP0048312 (Phytuberin)