NP-MRD: Showing NP-Card for Bacillariolide II (NP0050342)

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Record Information

Version

2.0

Created at

2022-04-27 20:54:03 UTC

Updated at

2022-04-27 20:54:03 UTC

NP-MRD ID

NP0050342

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Bacillariolide II

Description

(3S,3aS,4R,6aS)-4-hydroxy-3-[(1Z,4Z,7Z,10Z)-trideca-1,4,7,10-tetraen-1-yl]-hexahydro-1H-cyclopenta[c]furan-1-one belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. Bacillariolide II is found in Nitzschia pungens. Based on a literature review very few articles have been published on (3S,3aS,4R,6aS)-4-hydroxy-3-[(1Z,4Z,7Z,10Z)-trideca-1,4,7,10-tetraen-1-yl]-hexahydro-1H-cyclopenta[c]furan-1-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304272222542D          

 23 24  0  0  1  0            999 V2000
   -2.6759   -2.6341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1238   -3.2472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3788   -4.0318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8267   -4.6449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0198   -4.4734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4677   -5.0865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3392   -4.9149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5942   -4.1303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4012   -3.9588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6561   -3.1742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1041   -2.5611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971   -2.7326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.3349    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7846   -1.0799    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2549    0.7846    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849   -0.6674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692   -1.3349    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8242   -2.1195    0.0000 O   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  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
 14 13  1  6  0  0  0
 15 14  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 14 19  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0050342

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C/C\C=C/C\C=C/C\C=C/[C@@H]1OC(=O)[C@H]2CC[C@@H](O)[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-18-19-16(20(22)23-18)14-15-17(19)21/h3-4,6-7,9-10,12-13,16-19,21H,2,5,8,11,14-15H2,1H3/b4-3-,7-6-,10-9-,13-12-/t16-,17+,18-,19-/m0/s1

> <INCHI_KEY>
MUYSCJDPOFJXIF-ZDAITOFNSA-N

> <FORMULA>
C20H28O3

> <MOLECULAR_WEIGHT>
316.441

> <EXACT_MASS>
316.203844762

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
35.484413883536575

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,3aS,4R,6aS)-4-hydroxy-3-[(1Z,4Z,7Z,10Z)-trideca-1,4,7,10-tetraen-1-yl]-hexahydro-1H-cyclopenta[c]furan-1-one

> <ALOGPS_LOGP>
4.62

> <JCHEM_LOGP>
4.230764940666665

> <ALOGPS_LOGS>
-4.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.826496063474352

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8746906218363177

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
97.58990000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.78e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,3aS,4R,6aS)-4-hydroxy-3-[(1Z,4Z,7Z,10Z)-trideca-1,4,7,10-tetraen-1-yl]-hexahydrocyclopenta[c]furan-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  C   UNK     0      -4.995  -4.917   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.964  -6.061   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.440  -7.526   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.410  -8.670   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.904  -8.350   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.873  -9.495   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.633  -9.175   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.109  -7.710   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.615  -7.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.091  -5.925   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.061  -4.781   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.555  -5.101   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.476  -3.956   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.000  -2.492   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.465  -2.016   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.476   1.465   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.905  -1.246   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.929   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.929  -2.492   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       3.405  -3.956   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16   22                                                  
CONECT   16   15   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   14                                                       
CONECT   20   16   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   15   23                                                  
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₈O₃

Average Mass

316.4410 Da

Monoisotopic Mass

316.20384 Da

IUPAC Name

(3S,3aS,4R,6aS)-4-hydroxy-3-[(1Z,4Z,7Z,10Z)-trideca-1,4,7,10-tetraen-1-yl]-hexahydro-1H-cyclopenta[c]furan-1-one

Traditional Name

(3S,3aS,4R,6aS)-4-hydroxy-3-[(1Z,4Z,7Z,10Z)-trideca-1,4,7,10-tetraen-1-yl]-hexahydrocyclopenta[c]furan-1-one

CAS Registry Number

Not Available

SMILES

CC\C=C/C\C=C/C\C=C/C\C=C/[C@@H]1OC(=O)[C@H]2CC[C@@H](O)[C@@H]12

InChI Identifier

InChI=1S/C20H28O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-18-19-16(20(22)23-18)14-15-17(19)21/h3-4,6-7,9-10,12-13,16-19,21H,2,5,8,11,14-15H2,1H3/b4-3-,7-6-,10-9-,13-12-/t16-,17+,18-,19-/m0/s1

InChI Key

MUYSCJDPOFJXIF-ZDAITOFNSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Nitzschia pungens	Chromalveolata	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Gamma butyrolactones

Direct Parent

Gamma butyrolactones

Alternative Parents

Substituents

Gamma butyrolactone
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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	4.62	ALOGPS
logP	4.23	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	14.83	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	46.53 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	97.59 m³·mol⁻¹	ChemAxon
Polarizability	35.48 Å³	ChemAxon
Number of Rings	2	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

9442080

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11267069

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Bacillariolide II (NP0050342)

MOL for NP0050342 (Bacillariolide II)

3D MOL for NP0050342 (Bacillariolide II)

3D SDF for NP0050342 (Bacillariolide II)

3D-SDF for NP0050342 (Bacillariolide II)

PDB for NP0050342 (Bacillariolide II)

3D PDB for NP0050342 (Bacillariolide II)

SMILES for NP0050342 (Bacillariolide II)

INCHI for NP0050342 (Bacillariolide II)

Structure for NP0050342 (Bacillariolide II)

3D Structure for NP0050342 (Bacillariolide II)