NP-MRD: Showing NP-Card for Sambucinol (NP0059128)

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Record Information

Version

2.0

Created at

2022-04-28 04:24:23 UTC

Updated at

2022-04-28 04:24:23 UTC

NP-MRD ID

NP0059128

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sambucinol

Description

(1R,6S,7R,9S,10R,11R)-11-(hydroxymethyl)-3,6,7-trimethyl-12,13-dioxatetracyclo[8.2.1.0¹,⁶.0⁷,¹¹]Tridec-2-en-9-ol 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. Sambucinol is found in Fusarium culmorum, Fusarium sambusinum and Fusarium sporotrichioides. Based on a literature review very few articles have been published on (1R,6S,7R,9S,10R,11R)-11-(hydroxymethyl)-3,6,7-trimethyl-12,13-dioxatetracyclo[8.2.1.0¹,⁶.0⁷,¹¹]Tridec-2-en-9-ol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 41 44  0  0  0  0  0  0  0  0999 V2000
    4.4082   -0.1971   -0.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9534    0.0563   -0.1608 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1040    0.0540   -1.2118 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7178    0.3032   -0.9024 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3291    1.6089   -0.8284 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0801    1.5665   -0.9181 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5925    1.9785    0.4449 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8365    2.6039    0.2999 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6885    0.6924    1.2011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1096   -0.3986    0.3541 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7909   -1.6973    0.6340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3751   -0.4873    0.3728 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8751   -1.8974    0.2073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0758    0.1580    1.4910 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5376    0.2914    1.2189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3577    0.1101   -1.0472 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6260   -0.2808   -1.6479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6735    0.1675   -0.8791 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2137   -0.3105   -1.7730 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5395   -0.7319   -1.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8758   -0.8031    0.3705 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8907    0.7999   -0.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5015   -0.1310   -2.2088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4305    2.1937   -1.7333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9365    2.7088    0.9493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7152    3.3351   -0.3406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7905    0.4627    1.3023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3055    0.7293    2.2279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5522   -2.4353   -0.1563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4917   -2.0248    1.6494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8915   -1.5237    0.6919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2455   -2.6360    0.7799 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8748   -2.1253   -0.8793 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8908   -2.0074    0.6534 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6502    1.1314    1.8169 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9762   -0.5084    2.3991 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8702    1.3312    1.4962 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1645   -0.3734    1.8761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6422   -1.3777   -1.8043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7204    0.1766   -2.6467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4104   -0.5123   -0.9562 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  1
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  6
 10 12  1  0
 12 13  1  6
 12 14  1  0
 14 15  1  0
 10 16  1  0
 16 17  1  6
 17 18  1  0
 16 19  1  0
 15  2  1  0
 12  4  1  0
 19  4  1  0
 16  6  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  6 24  1  6
  7 25  1  1
  8 26  1  0
  9 27  1  0
  9 28  1  0
 11 29  1  0
 11 30  1  0
 11 31  1  0
 13 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 17 39  1  0
 17 40  1  0
 18 41  1  0
M  END


  Mrv1652304282206242D          

 19 22  0  0  1  0            999 V2000
    2.8967    2.1907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2160    1.6403    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2101    0.7417    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0609    0.5696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7500    1.0643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6634    1.8838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5356    0.7185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7414   -0.0082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7927    0.5258    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2190    1.1016    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4055    1.8575    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5722    2.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2102    1.2343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6820    1.3642    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2769    2.7498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3539    0.2760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5099    1.5008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0955    0.7197    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1918    2.5452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  3  8  1  0  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  1  1  0  0  0
 11 15  1  1  0  0  0
 10 16  1  0  0  0  0
  3 16  1  1  0  0  0
 10 17  1  1  0  0  0
 17 18  1  0  0  0  0
  2 19  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0059128

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C[C@]23O[C@@H]4[C@@H](O)C[C@](C)([C@]2(C)CC1)[C@]4(CO)O3

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O4/c1-9-4-5-12(2)13(3)7-10(17)11-14(13,8-16)19-15(12,6-9)18-11/h6,10-11,16-17H,4-5,7-8H2,1-3H3/t10-,11+,12-,13+,14+,15+/m0/s1

> <INCHI_KEY>
GFLMBFRNOPTZDK-XWSJDDSLSA-N

> <FORMULA>
C15H22O4

> <MOLECULAR_WEIGHT>
266.337

> <EXACT_MASS>
266.151809188

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
28.77465223777918

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,6S,7R,9S,10R,11R)-11-(hydroxymethyl)-3,6,7-trimethyl-12,13-dioxatetracyclo[8.2.1.0^{1,6}.0^{7,11}]tridec-2-en-9-ol

> <ALOGPS_LOGP>
0.64

> <JCHEM_LOGP>
1.504832046666666

> <ALOGPS_LOGS>
-1.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.481006434238473

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.852909877832598

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1241556145132403

> <JCHEM_POLAR_SURFACE_AREA>
58.92

> <JCHEM_REFRACTIVITY>
69.2818

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.69e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,6S,7R,9S,10R,11R)-11-(hydroxymethyl)-3,6,7-trimethyl-12,13-dioxatetracyclo[8.2.1.0^{1,6}.0^{7,11}]tridec-2-en-9-ol

> <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       5.407   4.089   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.137   3.062   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.125   1.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.714   1.063   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.000   1.987   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.838   3.516   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.466   1.341   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.251  -0.015   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.480   0.981   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.275   2.056   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.624   3.467   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.068   3.776   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.392   2.304   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.273   2.546   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.384   5.133   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.527   0.515   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.952   2.801   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.178   1.344   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.091   4.751   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   11   19                                             
CONECT    3    2    4    8   16                                             
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    3    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11   16   17                                             
CONECT   11   10    2   12   15                                             
CONECT   12   11   13                                                       
CONECT   13   12    9   14                                                  
CONECT   14   13                                                            
CONECT   15   11                                                            
CONECT   16   10    3                                                       
CONECT   17   10   18                                                       
CONECT   18   17                                                            
CONECT   19    2                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₂O₄

Average Mass

266.3370 Da

Monoisotopic Mass

266.15181 Da

IUPAC Name

(1R,6S,7R,9S,10R,11R)-11-(hydroxymethyl)-3,6,7-trimethyl-12,13-dioxatetracyclo[8.2.1.0^{1,6}.0^{7,11}]tridec-2-en-9-ol

Traditional Name

(1R,6S,7R,9S,10R,11R)-11-(hydroxymethyl)-3,6,7-trimethyl-12,13-dioxatetracyclo[8.2.1.0^{1,6}.0^{7,11}]tridec-2-en-9-ol

CAS Registry Number

Not Available

SMILES

CC1=C[C@]23O[C@@H]4[C@@H](O)C[C@](C)([C@]2(C)CC1)[C@]4(CO)O3

InChI Identifier

InChI=1S/C15H22O4/c1-9-4-5-12(2)13(3)7-10(17)11-14(13,8-16)19-15(12,6-9)18-11/h6,10-11,16-17H,4-5,7-8H2,1-3H3/t10-,11+,12-,13+,14+,15+/m0/s1

InChI Key

GFLMBFRNOPTZDK-XWSJDDSLSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Fusarium culmorum	LOTUS Database	35616633
Fusarium sambusinum	Fungi	KNApSAcK
Fusarium sporotrichioides	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

Ketal
Oxepane
Oxane
Tetrahydrofuran
Cyclic alcohol
Meta-dioxolane
Secondary alcohol
Oxacycle
Acetal
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
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	0.64	ALOGPS
logP	1.5	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	13.85	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.92 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.28 m³·mol⁻¹	ChemAxon
Polarizability	28.77 Å³	ChemAxon
Number of Rings	4	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

163077371

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Sambucinol (NP0059128)

MOL for NP0059128 (Sambucinol)

3D MOL for NP0059128 (Sambucinol)

3D SDF for NP0059128 (Sambucinol)

3D-SDF for NP0059128 (Sambucinol)

PDB for NP0059128 (Sambucinol)

3D PDB for NP0059128 (Sambucinol)

SMILES for NP0059128 (Sambucinol)

INCHI for NP0059128 (Sambucinol)

Structure for NP0059128 (Sambucinol)

3D Structure for NP0059128 (Sambucinol)