NP-MRD: Showing NP-Card for Sinulobatin D (NP0332358)

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Record Information

Version

2.0

Created at

2024-01-11 16:08:47 UTC

Updated at

2024-09-03 04:18:56 UTC

NP-MRD ID

NP0332358

Natural Product DOI

https://doi.org/10.57994/1573

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sinulobatin D

Description

Sinulobatin D belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Sinulobatin D was first documented in 2024 (PMID: 38159620). Based on a literature review very few articles have been published on Sinulobatin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01112416082D          

 31 34  0  0  1  0            999 V2000
   -1.4570    1.1197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4570    2.1803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.9355    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8250    0.2211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.9355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.9355    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    0.2211    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.2211    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -0.4934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.2079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.2079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -1.9224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.2211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0625   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.9355    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    2.3645    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3000    3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2375    0.9355    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    3.0789    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
  2  4  1  0  0  0  0
  5  2  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
 10  5  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  1  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 23 22  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 19 26  1  0  0  0  0
 27 26  1  0  0  0  0
 10 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
  3 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 25 31  1  0  0  0  0
M  END


  Mrv2104 01112416082D          

 31 34  0  0  1  0            999 V2000
   -1.4570    1.1197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4570    2.1803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.9355    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8250    0.2211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.9355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.9355    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    0.2211    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.2211    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -0.4934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.2079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.2079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -1.9224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.2211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0625   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.9355    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    2.3645    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3000    3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2375    0.9355    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    3.0789    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
  2  4  1  0  0  0  0
  5  2  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
 10  5  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  1  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 23 22  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 19 26  1  0  0  0  0
 27 26  1  0  0  0  0
 10 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
  3 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 25 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332358

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CC[C@H](C)C3=C1[C@@]1([H])C(CC(C)(C)[C@@H](OC(C)=O)[C@]1([H])[C@@H](OC(C)=O)[C@@H]2C)=CC3

> <INCHI_IDENTIFIER>
InChI=1S/C24H34O4/c1-12-7-9-18-13(2)22(27-14(3)25)21-19-16(8-10-17(12)20(18)19)11-24(5,6)23(21)28-15(4)26/h8,12-13,18-19,21-23H,7,9-11H2,1-6H3/t12-,13+,18+,19+,21-,22-,23-/m0/s1

> <INCHI_KEY>
NOEYXOCPONNRST-OQVOSMCWSA-N

> <FORMULA>
C24H34O4

> <MOLECULAR_WEIGHT>
386.532

> <EXACT_MASS>
386.245709575

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
43.967409780881106

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,3a^{1}R,6S,8aR,9R,10S,10aS)-10-(acetyloxy)-2,2,6,9-tetramethyl-1,2,3,3a^{1},5,6,7,8,8a,9,10,10a-dodecahydropyren-1-yl acetate

> <JCHEM_LOGP>
3.5450965553333336

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.7033364488870815

> <JCHEM_POLAR_SURFACE_AREA>
52.6

> <JCHEM_REFRACTIVITY>
108.68449999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3a^{1}R,6S,8aR,9R,10S,10aS)-10-(acetyloxy)-2,2,6,9-tetramethyl-3,3a^{1},5,6,7,8,8a,9,10,10a-decahydro-1H-pyren-1-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-JAN-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-JAN-24         0                                  
HETATM    1  C   UNK     0      -2.720   2.090   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.540   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.770   4.414   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.720   4.070   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770   1.746   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.540   0.413   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.080   0.413   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.850  -0.921   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.850   1.746   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.770   1.746   0.000  0.00  0.00           C+0
HETATM   11  H   UNK     0      -0.000   0.413   0.000  0.00  0.00           H+0
HETATM   12  C   UNK     0       1.540   0.413   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.770  -0.921   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.540  -2.255   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.080  -2.255   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.770  -3.588   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       3.080   0.413   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.850  -0.921   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.850   1.746   0.000  0.00  0.00           C+0
HETATM   20  H   UNK     0       4.620   3.080   0.000  0.00  0.00           H+0
HETATM   21  C   UNK     0       5.390   1.746   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.160   3.080   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.390   4.414   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.160   5.747   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.850   4.414   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.080   3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.540   3.080   0.000  0.00  0.00           C+0
HETATM   28  H   UNK     0       2.310   1.746   0.000  0.00  0.00           H+0
HETATM   29  C   UNK     0       0.770   4.414   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.540   5.747   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.080   5.747   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2   29                                                       
CONECT    4    2                                                            
CONECT    5    2    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5   11   12   27                                             
CONECT   11   10                                                            
CONECT   12   10   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   12   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21   26                                             
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   31                                                  
CONECT   26   25   19   27                                                  
CONECT   27   26   10   28   29                                             
CONECT   28   27                                                            
CONECT   29   27    3   30                                                  
CONECT   30   29   31                                                       
CONECT   31   30   25                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₄O₄

Average Mass

386.5320 Da

Monoisotopic Mass

386.24571 Da

IUPAC Name

(1S,3a^{1}R,6S,8aR,9R,10S,10aS)-10-(acetyloxy)-2,2,6,9-tetramethyl-1,2,3,3a^{1},5,6,7,8,8a,9,10,10a-dodecahydropyren-1-yl acetate

Traditional Name

(1S,3a^{1}R,6S,8aR,9R,10S,10aS)-10-(acetyloxy)-2,2,6,9-tetramethyl-3,3a^{1},5,6,7,8,8a,9,10,10a-decahydro-1H-pyren-1-yl acetate

CAS Registry Number

Not Available

SMILES

[H][C@]12CC[C@H](C)C3=C1[C@@]1([H])C(CC(C)(C)[C@@H](OC(C)=O)[C@]1([H])[C@@H](OC(C)=O)[C@@H]2C)=CC3

InChI Identifier

InChI=1S/C24H34O4/c1-12-7-9-18-13(2)22(27-14(3)25)21-19-16(8-10-17(12)20(18)19)11-24(5,6)23(21)28-15(4)26/h8,12-13,18-19,21-23H,7,9-11H2,1-6H3/t12-,13+,18+,19+,21-,22-,23-/m0/s1

InChI Key

NOEYXOCPONNRST-OQVOSMCWSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400.13280091, CDCl₃, simulated)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-05-02	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
brassica		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Fatty alcohol ester
Dicarboxylic acid or derivatives
Carboxylic acid ester
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	3.55	ChemAxon
pKa (Strongest Basic)	-6.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	52.6 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	108.68 m³·mol⁻¹	ChemAxon
Polarizability	43.97 Å³	ChemAxon
Number of Rings	4	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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Xia ZY, Sun MM, Jin Y, Su MZ, Li SW, Wang H, Guo YW: Four uncommon cycloamphilectane-type diterpenoids with antibacterial activity from the South China Sea soft coral Sinularia brassica. Phytochemistry. 2024 Mar;219:113960. doi: 10.1016/j.phytochem.2023.113960. Epub 2023 Dec 29. [PubMed:38159620 ]

Showing NP-Card for Sinulobatin D (NP0332358)

MOL for NP0332358 (Sinulobatin D)

3D MOL for NP0332358 (Sinulobatin D)

3D SDF for NP0332358 (Sinulobatin D)

3D-SDF for NP0332358 (Sinulobatin D)

PDB for NP0332358 (Sinulobatin D)

3D PDB for NP0332358 (Sinulobatin D)

SMILES for NP0332358 (Sinulobatin D)

INCHI for NP0332358 (Sinulobatin D)

Structure for NP0332358 (Sinulobatin D)

3D Structure for NP0332358 (Sinulobatin D)