NP-MRD: Showing NP-Card for 12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one (NP0249050)

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Record Information

Version

2.0

Created at

2022-09-07 11:30:19 UTC

Updated at

2022-09-07 11:30:19 UTC

NP-MRD ID

NP0249050

Secondary Accession Numbers

None

Natural Product Identification

Common Name

12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one

Description

12-(Hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]Tetradeca-7,11-dien-13-one belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. 12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one is found in Pentzia pinnatisecta. 12-(Hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]Tetradeca-7,11-dien-13-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
   -0.7587    2.0473   -1.5132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1530    1.4739   -0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1107    0.5625   -0.1835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7188   -0.1815    0.9267 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5923   -1.7103    0.8191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1102   -2.0895    0.5048 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8975   -3.5445    0.3228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6932   -1.1506   -0.3847 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2846   -1.1407    0.9510 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1995   -0.9506    0.8545 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8474   -1.7746   -0.0079 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5215   -1.0309   -0.9253 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2349   -1.4755   -1.8882 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2786    0.3515   -0.6056 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8297    1.5291   -1.3566 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2246    1.4900   -1.3251 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4970    0.4388    0.4493 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9735    1.6351    1.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4395    1.9649    1.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3365    3.0859   -1.3830 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0088    1.4680   -2.0249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6712    2.2148   -2.1564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5417    0.2995   -1.1722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5305    0.2012    1.9326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8432   -0.0338    0.8145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8164   -2.0995    1.8339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2466   -2.1149    0.0431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6718   -4.1071    0.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0052   -3.8677   -0.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0834   -3.9004    0.7469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6489   -0.4849    1.7404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6162   -1.1562    1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4409    2.4692   -0.9550 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4441    1.4203   -2.4005 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5971    1.2478   -2.2269 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6054    2.5414    0.9474 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2496    1.4247    2.2541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5175    3.1057    0.9445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0640    1.8419    1.9494 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  6
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 14 17  2  0
 17 18  1  0
 18 19  1  0
 19  2  1  0
  9  6  1  0
 17 10  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  7 30  1  0
  9 31  1  1
 10 32  1  1
 15 33  1  0
 15 34  1  0
 16 35  1  0
 18 36  1  0
 18 37  1  0
 19 38  1  0
 19 39  1  0
M  END


  Mrv1533004201500252D          

 19 21  0  0  0  0            999 V2000
    0.6546    4.9851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0050    4.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8271    4.1682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774    3.4213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7058    2.7444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0562    1.9975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8031    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4066    1.2506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5846    1.3206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7626    1.3906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1605    0.8266    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5620    1.2249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3089    0.8745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4065    2.0351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4122    2.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.8144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5334    3.5613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9705    2.6371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7739    2.4497    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  4  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  6  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  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  2 17  1  0  0  0  0
 14 18  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0249050

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CCCC2(C)OC2C2OC(=O)C(CO)=C2CC1

> <INCHI_IDENTIFIER>
InChI=1S/C15H20O4/c1-9-4-3-7-15(2)13(19-15)12-10(6-5-9)11(8-16)14(17)18-12/h4,12-13,16H,3,5-8H2,1-2H3

> <INCHI_KEY>
VKVLIZXYYIZTGG-UHFFFAOYSA-N

> <FORMULA>
C15H20O4

> <MOLECULAR_WEIGHT>
264.321

> <EXACT_MASS>
264.136159124

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
28.140848768569988

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one

> <ALOGPS_LOGP>
1.79

> <JCHEM_LOGP>
1.7668836766666667

> <ALOGPS_LOGS>
-2.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.957540733497328

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.210573202439784

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8597845430477022

> <JCHEM_POLAR_SURFACE_AREA>
59.06

> <JCHEM_REFRACTIVITY>
71.0565

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.46e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  C   UNK     0       1.222   9.306   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.876   7.911   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.410   7.781   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.065   6.386   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.184   5.123   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.838   3.729   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.232   4.383   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.492   2.335   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.958   2.465   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.423   2.596   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.300   1.543   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.049   2.286   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.443   1.632   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.759   3.799   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.769   3.990   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.650   5.254   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.996   6.648   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.812   4.923   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -3.311   4.573   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    6   10                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   18                                                  
CONECT   15   14   10   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16    2                                                       
CONECT   18   14   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₀O₄

Average Mass

264.3210 Da

Monoisotopic Mass

264.13616 Da

IUPAC Name

12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one

Traditional Name

12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one

CAS Registry Number

Not Available

SMILES

CC1=CCCC2(C)OC2C2OC(=O)C(CO)=C2CC1

InChI Identifier

InChI=1S/C15H20O4/c1-9-4-3-7-15(2)13(19-15)12-10(6-5-9)11(8-16)14(17)18-12/h4,12-13,16H,3,5-8H2,1-2H3

InChI Key

VKVLIZXYYIZTGG-UHFFFAOYSA-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
Pentzia pinnatisecta	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Germacranolides and derivatives

Alternative Parents

Substituents

Germacranolide
Germacrane sesquiterpenoid
Sesquiterpenoid
2-furanone
Dihydrofuran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Lactone
Monocarboxylic acid or derivatives
Oxacycle
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organoheterocyclic compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
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	1.79	ALOGPS
logP	1.77	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	11.21	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	59.06 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	71.06 m³·mol⁻¹	ChemAxon
Polarizability	28.14 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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one (NP0249050)

MOL for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

3D MOL for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

3D SDF for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

3D-SDF for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

PDB for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

3D PDB for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

SMILES for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

INCHI for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

Structure for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)

3D Structure for NP0249050 (12-(hydroxymethyl)-4,8-dimethyl-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradeca-7,11-dien-13-one)