NP-MRD: Showing NP-Card for 6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione (NP0247920)

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Record Information

Version

2.0

Created at

2022-09-07 09:56:45 UTC

Updated at

2022-09-07 09:56:45 UTC

NP-MRD ID

NP0247920

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione

Description

Pandangolide 4 belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members. Pandangolide 4 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171500142D          

 33 34  0  0  0  0            999 V2000
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 32 33  2  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1533004171500142D          

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M  END
> <DATABASE_ID>
NP0247920

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1CCCCCC(O)C(=O)C(CC(=O)O1)SC1CC(=O)OC(C)CCCCCC(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H38O8S/c1-15-9-5-3-7-11-17(25)23(29)19(13-21(27)31-15)33-20-14-22(28)32-16(2)10-6-4-8-12-18(26)24(20)30/h15-20,25-26H,3-14H2,1-2H3

> <INCHI_KEY>
NUPJXSWNOKBNII-UHFFFAOYSA-N

> <FORMULA>
C24H38O8S

> <MOLECULAR_WEIGHT>
486.62

> <EXACT_MASS>
486.228739358

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
51.16238006288316

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione

> <ALOGPS_LOGP>
2.09

> <JCHEM_LOGP>
3.463395610333332

> <ALOGPS_LOGS>
-3.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.696175439768858

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.318975490281922

> <JCHEM_PKA_STRONGEST_BASIC>
-3.509390543146969

> <JCHEM_POLAR_SURFACE_AREA>
127.19999999999999

> <JCHEM_REFRACTIVITY>
123.47569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.06e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -1.810  -4.032   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.810  -2.492   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.477  -1.722   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.857  -2.492   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.857  -4.032   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.477  -4.802   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.477  -6.342   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.810  -7.112   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.810  -8.652   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -3.144  -6.342   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -4.478  -7.112   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -3.144  -4.802   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.478  -4.032   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.478  -2.492   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -5.811  -1.722   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -3.144  -1.722   0.000  0.00  0.00           O+0
HETATM   17  S   UNK     0      -4.478  -5.572   0.000  0.00  0.00           S+0
HETATM   18  C   UNK     0      -6.009  -5.733   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.104  -6.979   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.730  -8.385   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -4.825  -9.631   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -7.262  -8.546   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -8.167  -7.301   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -7.541  -5.894   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -9.699  -7.462   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -10.604  -6.216   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -9.978  -4.809   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -8.446  -4.648   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -7.820  -3.241   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.288  -3.080   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -6.608  -1.574   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -5.383  -4.326   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -5.063  -2.820   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    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   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14    2                                                       
CONECT   17   12   18                                                       
CONECT   18   17   19   32                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   18   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₈O₈S

Average Mass

486.6200 Da

Monoisotopic Mass

486.22874 Da

IUPAC Name

6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione

Traditional Name

6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione

CAS Registry Number

Not Available

SMILES

CC1CCCCCC(O)C(=O)C(CC(=O)O1)SC1CC(=O)OC(C)CCCCCC(O)C1=O

InChI Identifier

InChI=1S/C24H38O8S/c1-15-9-5-3-7-11-17(25)23(29)19(13-21(27)31-15)33-20-14-22(28)32-16(2)10-6-4-8-12-18(26)24(20)30/h15-20,25-26H,3-14H2,1-2H3

InChI Key

NUPJXSWNOKBNII-UHFFFAOYSA-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 macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Not Available

Direct Parent

Macrolides and analogues

Alternative Parents

Substituents

Macrolide
Dicarboxylic acid or derivatives
Carboxylic acid ester
Ketone
Lactone
Secondary alcohol
Cyclic ketone
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Dialkylthioether
Thioether
Sulfenyl compound
Hydrocarbon derivative
Carbonyl group
Organooxygen compound
Organosulfur compound
Alcohol
Organic oxygen compound
Organic oxide
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	2.09	ALOGPS
logP	3.46	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	11.32	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	127.2 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	123.48 m³·mol⁻¹	ChemAxon
Polarizability	51.16 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

10791120

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione (NP0247920)

MOL for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

3D MOL for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

3D SDF for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

3D-SDF for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

PDB for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

3D PDB for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

SMILES for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

INCHI for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

Structure for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)

3D Structure for NP0247920 (6-hydroxy-4-[(6-hydroxy-12-methyl-2,5-dioxo-1-oxacyclododecan-4-yl)sulfanyl]-12-methyl-1-oxacyclododecane-2,5-dione)