NP-MRD: Showing NP-Card for caloundrin b (NP0256578)

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Record Information

Version

2.0

Created at

2022-09-07 21:27:30 UTC

Updated at

2022-09-07 21:27:30 UTC

NP-MRD ID

NP0256578

Secondary Accession Numbers

None

Natural Product Identification

Common Name

caloundrin b

Description

Caloundrin B belongs to the class of organic compounds known as pyranones and derivatives. Pyranones and derivatives are compounds containing a pyran ring which bears a ketone. caloundrin b is found in Siphonaria zelandica. caloundrin b was first documented in 2009 (PMID: 19281137). Based on a literature review a small amount of articles have been published on Caloundrin B (PMID: 20441190) (PMID: 22369698).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072223272D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309072223272D          

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   -0.5770   -6.6086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0059   -6.6087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0059   -7.4337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7204   -6.1962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4349   -6.6087    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  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 16 14  1  6  0  0  0
 16 17  1  0  0  0  0
 18 17  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  1  0  0  0  0
 16 31  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 21 31  1  0  0  0  0
 27 28  1  6  0  0  0
 25 29  1  0  0  0  0
 16 29  1  0  0  0  0
 29 30  1  6  0  0  0
 18 27  1  0  0  0  0
 21 24  1  0  0  0  0
  5 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
  3 36  2  0  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0256578

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC1=C(C)C(=O)C(C)=C(O1)[C@@H](C)C(=O)[C@H](C)[C@H](O)[C@H](C)[C@@]12O[C@@H]3[C@H](C)[C@@](O)(O[C@](CC)(O1)[C@H]3C)[C@H]2C

> <INCHI_IDENTIFIER>
InChI=1S/C29H44O8/c1-11-21-13(3)22(30)15(5)25(34-21)16(6)23(31)14(4)24(32)17(7)29-20(10)28(33)19(9)26(35-29)18(8)27(12-2,36-28)37-29/h14,16-20,24,26,32-33H,11-12H2,1-10H3/t14-,16-,17-,18-,19-,20+,24-,26-,27+,28+,29+/m0/s1

> <INCHI_KEY>
DZCOUGLKWPXZPW-YUAAGDMFSA-N

> <FORMULA>
C29H44O8

> <MOLECULAR_WEIGHT>
520.663

> <EXACT_MASS>
520.303618377

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
57.06904195905501

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-ethyl-6-[(2R,4R,5S,6S)-6-[(1R,3R,5R,7R,8S,9S,10R)-5-ethyl-7-hydroxy-8,9,10-trimethyl-2,4,6-trioxatricyclo[3.3.1.1^{3,7}]decan-3-yl]-5-hydroxy-4-methyl-3-oxoheptan-2-yl]-3,5-dimethyl-4H-pyran-4-one

> <JCHEM_LOGP>
6.177634115333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.724612279396553

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.344106252595026

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0762123031233344

> <JCHEM_POLAR_SURFACE_AREA>
111.52000000000001

> <JCHEM_REFRACTIVITY>
139.02380000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-ethyl-6-[(2R,4R,5S,6S)-6-[(1R,3R,5R,7R,8S,9S,10R)-5-ethyl-7-hydroxy-8,9,10-trimethyl-2,4,6-trioxatricyclo[3.3.1.1^{3,7}]decan-3-yl]-5-hydroxy-4-methyl-3-oxoheptan-2-yl]-3,5-dimethylpyran-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      -7.746 -10.026   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.412  -9.256   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.078 -10.026   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -3.745  -9.256   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.411 -10.026   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.077  -9.256   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.257 -10.026   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.077  -7.716   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.411  -6.946   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.256  -6.946   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.590  -7.716   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.256  -5.406   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.077  -4.636   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.590  -4.636   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.924  -5.406   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.590  -3.096   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.217  -3.793   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.056  -2.318   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.429  -3.016   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.429  -4.556   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.802  -2.318   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.291  -2.712   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.376  -1.620   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.802  -0.923   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.429  -0.225   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.429   1.315   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.056  -0.923   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.257  -0.118   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.590  -1.701   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.101  -1.307   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       2.963  -3.793   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.411 -11.566   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.077 -12.336   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -3.744 -12.336   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -3.744 -13.876   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -5.078 -11.566   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -6.412 -12.336   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   36                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   32                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   29   31                                             
CONECT   17   16   18                                                       
CONECT   18   17   19   27                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   24   31                                             
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21   25                                                       
CONECT   25   24   26   27   29                                             
CONECT   26   25                                                            
CONECT   27   25   18   28                                                  
CONECT   28   27                                                            
CONECT   29   25   16   30                                                  
CONECT   30   29                                                            
CONECT   31   21   16                                                       
CONECT   32    5   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34    3   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₄O₈

Average Mass

520.6630 Da

Monoisotopic Mass

520.30362 Da

IUPAC Name

2-ethyl-6-[(2R,4R,5S,6S)-6-[(1R,3R,5R,7R,8S,9S,10R)-5-ethyl-7-hydroxy-8,9,10-trimethyl-2,4,6-trioxatricyclo[3.3.1.1^{3,7}]decan-3-yl]-5-hydroxy-4-methyl-3-oxoheptan-2-yl]-3,5-dimethyl-4H-pyran-4-one

Traditional Name

2-ethyl-6-[(2R,4R,5S,6S)-6-[(1R,3R,5R,7R,8S,9S,10R)-5-ethyl-7-hydroxy-8,9,10-trimethyl-2,4,6-trioxatricyclo[3.3.1.1^{3,7}]decan-3-yl]-5-hydroxy-4-methyl-3-oxoheptan-2-yl]-3,5-dimethylpyran-4-one

CAS Registry Number

Not Available

SMILES

CCC1=C(C)C(=O)C(C)=C(O1)[C@@H](C)C(=O)[C@H](C)[C@H](O)[C@H](C)[C@@]12O[C@@H]3[C@H](C)[C@@](O)(O[C@](CC)(O1)[C@H]3C)[C@H]2C

InChI Identifier

InChI=1S/C29H44O8/c1-11-21-13(3)22(30)15(5)25(34-21)16(6)23(31)14(4)24(32)17(7)29-20(10)28(33)19(9)26(35-29)18(8)27(12-2,36-28)37-29/h14,16-20,24,26,32-33H,11-12H2,1-10H3/t14-,16-,17-,18-,19-,20+,24-,26-,27+,28+,29+/m0/s1

InChI Key

DZCOUGLKWPXZPW-YUAAGDMFSA-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
Siphonaria zelandica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyranones and derivatives. Pyranones and derivatives are compounds containing a pyran ring which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrans

Sub Class

Pyranones and derivatives

Direct Parent

Pyranones and derivatives

Alternative Parents

Substituents

Pyranone
Ketal
Meta-dioxane
Beta-hydroxy ketone
Oxane
Heteroaromatic compound
Cyclic ketone
Secondary alcohol
Ketone
Hemiacetal
Oxacycle
Acetal
Organic oxygen compound
Alcohol
Organooxygen compound
Carbonyl group
Aldehyde
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	6.18	ChemAxon
pKa (Strongest Acidic)	11.34	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	111.52 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	139.02 m³·mol⁻¹	ChemAxon
Polarizability	57.07 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

102423708

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Beye GE, Ward DE: On the origin of siphonariid polypropionates: total synthesis of baconipyrone A, baconipyrone C, and siphonarin B via their putative common precursor. J Am Chem Soc. 2010 May 26;132(20):7210-5. doi: 10.1021/ja102356j. [PubMed:20441190 ]
Beye GE, Goodman JM, Ward DE: Synthetic studies on siphonariid polypropionates: synthesis and isomerization of the caloundrin B trioxaadamantane ring system. Org Lett. 2009 Mar 19;11(6):1373-6. doi: 10.1021/ol900192q. [PubMed:19281137 ]
Becerril-Jimenez F, Ward DE: On the origin of siphonariid polypropionates: total synthesis of caloundrin B and its isomerization to siphonarin B. Org Lett. 2012 Mar 16;14(6):1648-51. doi: 10.1021/ol300432y. Epub 2012 Feb 27. [PubMed:22369698 ]
LOTUS database [Link]

Showing NP-Card for caloundrin b (NP0256578)

MOL for NP0256578 (caloundrin b)

3D MOL for NP0256578 (caloundrin b)

3D SDF for NP0256578 (caloundrin b)

3D-SDF for NP0256578 (caloundrin b)

PDB for NP0256578 (caloundrin b)

3D PDB for NP0256578 (caloundrin b)

SMILES for NP0256578 (caloundrin b)

INCHI for NP0256578 (caloundrin b)

Structure for NP0256578 (caloundrin b)

3D Structure for NP0256578 (caloundrin b)