NP-MRD: Showing NP-Card for (1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate (NP0235146)

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Record Information

Version

2.0

Created at

2022-09-06 17:36:41 UTC

Updated at

2022-09-06 17:36:41 UTC

NP-MRD ID

NP0235146

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate

Description

(1R,3R,4S,6R,8R,9R,12S)-4,8-dihydroxy-12-[(3R)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]Dodecan-3-yl (2Z)-2-methylbut-2-enoate belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms. (1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate is found in Waitzia acuminata. Based on a literature review very few articles have been published on (1R,3R,4S,6R,8R,9R,12S)-4,8-dihydroxy-12-[(3R)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]Dodecan-3-yl (2Z)-2-methylbut-2-enoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062219362D          

 31 33  0  0  1  0            999 V2000
    1.9523   -4.5461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1079   -3.7359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4840   -3.1961    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0239   -2.5722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9442   -3.8200    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8602   -2.6563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0408   -1.7155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.7101   -1.3893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0107    1.6505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2166    1.8740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3978    3.0260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6037    3.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9021    0.1469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
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 23 31  1  0  0  0  0
  9 31  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309062219362D          

 31 33  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0235146

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C(\C)C(=O)O[C@@H]1C[C@]23CO[C@](C)([C@H]2CC[C@@](C)(O)C=C)[C@H](O)C[C@H]3C(C)(C)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H40O6/c1-8-15(3)21(28)31-16-13-25-14-30-24(7,17(25)10-11-23(6,29)9-2)19(26)12-18(25)22(4,5)20(16)27/h8-9,16-20,26-27,29H,2,10-14H2,1,3-7H3/b15-8-/t16-,17-,18+,19-,20-,23+,24-,25+/m1/s1

> <INCHI_KEY>
ZMNKLCLHIVLKBM-SXTIOAOKSA-N

> <FORMULA>
C25H40O6

> <MOLECULAR_WEIGHT>
436.589

> <EXACT_MASS>
436.282489008

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
48.17735149612541

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3R,4S,6R,8R,9R,12S)-4,8-dihydroxy-12-[(3R)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0^{1,6}]dodecan-3-yl (2Z)-2-methylbut-2-enoate

> <JCHEM_LOGP>
3.0501095583333337

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.178232108924558

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.541882147774562

> <JCHEM_PKA_STRONGEST_BASIC>
-1.374626665508032

> <JCHEM_POLAR_SURFACE_AREA>
96.22

> <JCHEM_REFRACTIVITY>
119.31579999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R,4S,6R,8R,9R,12S)-4,8-dihydroxy-12-[(3R)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0^{1,6}]dodecan-3-yl (2Z)-2-methylbut-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       3.644  -8.486   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.935  -6.974   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.770  -5.966   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.778  -4.802   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.762  -7.131   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.606  -4.958   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.943  -3.202   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.500  -1.722   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.617  -0.994   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.344   0.091   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.074  -0.698   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.234  -2.280   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.325  -2.593   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.922  -3.740   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.379  -4.787   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.523  -3.867   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.377  -2.465   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.948  -2.512   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.726  -3.950   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.344  -3.375   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.787  -1.206   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       7.350  -1.025   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.090   0.180   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       6.019   1.515   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.620   3.081   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       4.138   3.498   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.723   4.156   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.205   3.739   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.343   5.649   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.860   6.066   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.551   0.274   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   17   31                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8   13   14                                             
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16    9   18                                                  
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   31                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29                                                            
CONECT   31   23    9                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Value	Source
(1R,3R,4S,6R,8R,9R,12S)-4,8-Dihydroxy-12-[(3R)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0,]dodecan-3-yl (2Z)-2-methylbut-2-enoic acid	Generator

Chemical Formula

C₂₅H₄₀O₆

Average Mass

436.5890 Da

Monoisotopic Mass

436.28249 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C\C=C(\C)C(=O)O[C@@H]1C[C@]23CO[C@](C)([C@H]2CC[C@@](C)(O)C=C)[C@H](O)C[C@H]3C(C)(C)[C@@H]1O

InChI Identifier

InChI=1S/C25H40O6/c1-8-15(3)21(28)31-16-13-25-14-30-24(7,17(25)10-11-23(6,29)9-2)19(26)12-18(25)22(4,5)20(16)27/h8-9,16-20,26-27,29H,2,10-14H2,1,3-7H3/b15-8-/t16-,17-,18+,19-,20-,23+,24-,25+/m1/s1

InChI Key

ZMNKLCLHIVLKBM-SXTIOAOKSA-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
Waitzia acuminata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxepanes

Sub Class

Not Available

Direct Parent

Oxepanes

Alternative Parents

Substituents

Fatty acid ester
Oxepane
Fatty acyl
Cyclic alcohol
Tertiary alcohol
Tetrahydrofuran
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Oxacycle
Organic oxide
Organooxygen compound
Organic oxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
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

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

162988974

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate (NP0235146)

MOL for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

3D MOL for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

3D SDF for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

3D-SDF for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

PDB for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

3D PDB for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

SMILES for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

INCHI for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

Structure for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)

3D Structure for NP0235146 ((1r,3r,4s,6r,8r,9r,12s)-4,8-dihydroxy-12-[(3r)-3-hydroxy-3-methylpent-4-en-1-yl]-5,5,9-trimethyl-10-oxatricyclo[7.2.1.0¹,⁶]dodecan-3-yl (2z)-2-methylbut-2-enoate)