NP-MRD: Showing NP-Card for 3-deoxysambucinol (NP0172011)

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Record Information

Version

2.0

Created at

2022-09-03 08:46:23 UTC

Updated at

2022-09-03 08:46:23 UTC

NP-MRD ID

NP0172011

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-deoxysambucinol

Description

3-Deoxysambucinol 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. 3-deoxysambucinol was first documented in 2015 (PMID: 25633363). Based on a literature review very few articles have been published on 3-Deoxysambucinol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 43  0  0  0  0  0  0  0  0999 V2000
    4.1429    1.1986    0.7445 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7377    0.8378    0.3143 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8037    0.6134    1.2254 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4607    0.2684    0.8138 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3610   -0.2237    1.8037 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6908    0.1021    1.4522 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5056   -1.1338    1.1956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6587   -1.8023    0.1053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0625   -0.6292   -0.6778 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4418   -0.6807   -2.1133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4669    0.6142    0.0426 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5616    1.3880   -0.5234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9045    2.4275    0.3399 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2815    1.3502    0.2767 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4415   -0.6140   -0.4445 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0395   -1.9396   -0.2402 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1231    0.2196   -1.5035 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4564    0.7493   -1.1197 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2448    2.3053    0.7850 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3223    0.7196    1.7356 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8329    0.7726   -0.0137 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1324    0.7100    2.2735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1432    0.8243    2.1210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4442   -0.8290    0.7218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6127   -1.7604    2.0809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8598   -2.3464    0.6737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2622   -2.4540   -0.5310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7488   -0.1526   -2.7641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4598   -1.7680   -2.4159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4495   -0.2710   -2.2932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2477    1.8534   -1.4690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4501    0.7566   -0.6334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5166    3.0578   -0.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1952   -2.1292    0.8490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0831   -1.9274   -0.6762 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5329   -2.7847   -0.7513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4386    1.1008   -1.6806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2543   -0.3546   -2.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5924    1.7913   -1.5367 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2954    0.1398   -1.5715 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
  8  9  1  0
  9 10  1  6
  9 15  1  0
 15 16  1  1
 15 17  1  0
 17 18  1  0
  9 11  1  0
 11 12  1  6
 12 13  1  0
 11 14  1  0
 18  2  1  0
 15  4  1  0
 14  4  1  0
 11  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  6 23  1  1
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 10 28  1  0
 10 29  1  0
 10 30  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
 17 37  1  0
 17 38  1  0
 18 39  1  0
 18 40  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
M  END


  Mrv1652309032210462D          

 18 21  0  0  1  0            999 V2000
    3.2631    0.0400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5419    0.5099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7675    0.1858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9346    0.5985    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3598   -0.1066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5221    0.1439    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1602    0.7592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8443    1.5739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0181    1.6291    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2727    2.4771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2078    0.7331    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5290    0.3005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1144   -0.6191    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1722    1.1985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0241    1.4506    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2261    2.3401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8644    1.7444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6066    1.3180    0.0000 C   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  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
  4 14  1  1  0  0  0
  9 15  1  0  0  0  0
  4 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
  2 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0172011

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O3/c1-10-4-6-13(3)12(2)7-5-11-14(12,9-16)18-15(13,8-10)17-11/h8,11,16H,4-7,9H2,1-3H3/t11-,12-,13-,14-,15-/m1/s1

> <INCHI_KEY>
SFDJEINPFSNJBN-KJWHEZOQSA-N

> <FORMULA>
C15H22O3

> <MOLECULAR_WEIGHT>
250.338

> <EXACT_MASS>
250.156894568

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
27.695994421392086

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.03

> <JCHEM_LOGP>
2.579735653666666

> <ALOGPS_LOGS>
-2.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.261063718459575

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1220107295457815

> <JCHEM_POLAR_SURFACE_AREA>
38.69

> <JCHEM_REFRACTIVITY>
67.9203

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e+00 g/l

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

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       6.091   0.075   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.745   0.952   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.299   0.347   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.745   1.117   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.672  -0.199   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.975   0.269   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.166   1.417   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.576   2.938   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.034   3.041   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.509   4.624   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.388   1.368   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.987   0.561   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.214  -1.156   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.321   2.237   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.912   2.708   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.289   4.368   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.480   3.256   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.866   2.460   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   14   15                                             
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   15                                             
CONECT   10    9                                                            
CONECT   11    9    6   12   14                                             
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11    4                                                       
CONECT   15    9    4   16   17                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17    2                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₂O₃

Average Mass

250.3380 Da

Monoisotopic Mass

250.15689 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C15H22O3/c1-10-4-6-13(3)12(2)7-5-11-14(12,9-16)18-15(13,8-10)17-11/h8,11,16H,4-7,9H2,1-3H3/t11-,12-,13-,14-,15-/m1/s1

InChI Key

SFDJEINPFSNJBN-KJWHEZOQSA-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

Not Available

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
Meta-dioxolane
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	2.03	ALOGPS
logP	2.58	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	14.26	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	38.69 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	67.92 m³·mol⁻¹	ChemAxon
Polarizability	27.7 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

58827859

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

100969597

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wang Y, Zhang L, Li GT, Li ZH, Dong ZJ, Li Y, Liu JK: Identification and Cytotoxic Activities of Two New Trichothecenes and a New Cuparane-Type Sesquiterpenoid from the Cultures of the Mushroom Engleromyces goetzii. Nat Prod Bioprospect. 2015 Jan 30. doi: 10.1007/s13659-014-0051-1. [PubMed:25633363 ]
LOTUS database [Link]

Showing NP-Card for 3-deoxysambucinol (NP0172011)

MOL for NP0172011 (3-deoxysambucinol)

3D MOL for NP0172011 (3-deoxysambucinol)

3D SDF for NP0172011 (3-deoxysambucinol)

3D-SDF for NP0172011 (3-deoxysambucinol)

PDB for NP0172011 (3-deoxysambucinol)

3D PDB for NP0172011 (3-deoxysambucinol)

SMILES for NP0172011 (3-deoxysambucinol)

INCHI for NP0172011 (3-deoxysambucinol)

Structure for NP0172011 (3-deoxysambucinol)

3D Structure for NP0172011 (3-deoxysambucinol)