NP-MRD: Showing NP-Card for (3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione (NP0256583)

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Record Information

Version

2.0

Created at

2022-09-07 21:27:51 UTC

Updated at

2022-09-07 21:27:52 UTC

NP-MRD ID

NP0256583

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione

Description

Bis-osmundalactone belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. (3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione is found in Tapinella atrotomentosa. Based on a literature review very few articles have been published on Bis-osmundalactone.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309072223272D          

 18 18  0  0  1  0            999 V2000
    1.5395    2.8313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    2.0063    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3364    1.7928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9197    1.2094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6342    1.6219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1332    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9197   -0.3844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3364   -0.9678    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7489   -1.6822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -1.1813    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5395   -2.0063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7426   -0.9678    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1592   -0.3844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5553   -0.7969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0543    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1592    1.2094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7426    1.7928    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3301    2.5072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  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  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0256583

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H16O6/c1-7-9(13)3-5-12(16)18-8(2)10(14)4-6-11(15)17-7/h3-10,13-14H,1-2H3/b5-3-,6-4-/t7-,8-,9+,10+/m1/s1

> <INCHI_KEY>
LYHFOAGYEICQQA-HGILZDSQSA-N

> <FORMULA>
C12H16O6

> <MOLECULAR_WEIGHT>
256.254

> <EXACT_MASS>
256.094688235

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.47160217433197

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3Z,5S,6R,9Z,11S,12R)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione

> <JCHEM_LOGP>
0.6457113426666661

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.049573903732664

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.447489600713176

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3461814222468567

> <JCHEM_POLAR_SURFACE_AREA>
93.06000000000002

> <JCHEM_REFRACTIVITY>
63.25740000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3Z,5S,6R,9Z,11S,12R)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione

> <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       2.874   5.285   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.874   3.745   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.361   3.346   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.450   2.258   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.784   3.028   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.849   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.450  -0.718   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.361  -1.806   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.131  -3.140   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.874  -2.205   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.874  -3.745   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.386  -1.806   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.297  -0.718   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.036  -1.488   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.101   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.297   2.258   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.386   3.346   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.616   4.680   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    2   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₆O₆

Average Mass

256.2540 Da

Monoisotopic Mass

256.09469 Da

IUPAC Name

(3Z,5S,6R,9Z,11S,12R)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione

Traditional Name

(3Z,5S,6R,9Z,11S,12R)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C12H16O6/c1-7-9(13)3-5-12(16)18-8(2)10(14)4-6-11(15)17-7/h3-10,13-14H,1-2H3/b5-3-,6-4-/t7-,8-,9+,10+/m1/s1

InChI Key

LYHFOAGYEICQQA-HGILZDSQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Tapinella atrotomentosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Dicarboxylic acids and derivatives

Direct Parent

Dicarboxylic acids and derivatives

Alternative Parents

Substituents

Dicarboxylic acid or derivatives
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	0.65	ChemAxon
pKa (Strongest Acidic)	13.45	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	63.26 m³·mol⁻¹	ChemAxon
Polarizability	24.47 Å³	ChemAxon
Number of Rings	1	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

10232879

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21602025

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione (NP0256583)

MOL for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

3D MOL for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

3D SDF for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

3D-SDF for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

PDB for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

3D PDB for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

SMILES for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

INCHI for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

Structure for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)

3D Structure for NP0256583 ((3z,5s,6r,9z,11s,12r)-5,11-dihydroxy-6,12-dimethyl-1,7-dioxacyclododeca-3,9-diene-2,8-dione)