NP-MRD: Showing NP-Card for Sinucycloamtin C (NP0332360)

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Record Information

Version

2.0

Created at

2024-01-11 16:18:29 UTC

Updated at

2025-02-11 15:43:33 UTC

NP-MRD ID

NP0332360

Natural Product DOI

https://doi.org/10.57994/1575

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sinucycloamtin C

Description

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

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01112416182D          

 27 30  0  0  1  0            999 V2000
    2.5855   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3480   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1715   -0.1178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1715    0.9428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5395    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3020    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3480    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5855    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 13 10  1  0  0  0  0
 13 14  1  1  0  0  0
 15 13  1  0  0  0  0
 15  5  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24  4  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
  2 27  1  0  0  0  0
M  END


  Mrv2104 01112416182D          

 27 30  0  0  1  0            999 V2000
    2.5855   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3480   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1715   -0.1178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1715    0.9428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5395    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3020    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3480    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5855    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 13 10  1  0  0  0  0
 13 14  1  1  0  0  0
 15 13  1  0  0  0  0
 15  5  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24  4  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
  2 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332360

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CC[C@H](C)C3=C1C1=C(CC(C)(C)[C@@H](O)[C@]1([H])[C@@H](OC(C)=O)[C@@H]2C)C=C3

> <INCHI_IDENTIFIER>
InChI=1S/C22H30O3/c1-11-6-8-16-12(2)20(25-13(3)23)19-17-14(7-9-15(11)18(16)17)10-22(4,5)21(19)24/h7,9,11-12,16,19-21,24H,6,8,10H2,1-5H3/t11-,12+,16+,19-,20-,21-/m0/s1

> <INCHI_KEY>
ZLOCFCOPSPEISD-VEWXLAPWSA-N

> <FORMULA>
C22H30O3

> <MOLECULAR_WEIGHT>
342.479

> <EXACT_MASS>
342.219494826

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
39.72068568946959

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,3aR,4S,5R,5aR,8S)-3-hydroxy-2,2,5,8-tetramethyl-1,2,3,3a,4,5,5a,6,7,8-decahydropyren-4-yl acetate

> <JCHEM_LOGP>
4.170230930333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.311307112173756

> <JCHEM_PKA_STRONGEST_BASIC>
-3.100034269135199

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
98.52199999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,3aR,4S,5R,5aR,8S)-3-hydroxy-2,2,5,8-tetramethyl-3,3a,4,5,5a,6,7,8-octahydro-1H-pyren-4-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       4.826  -1.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.056  -0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.516  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.746   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.564  -0.564   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.206  -1.897   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.746  -1.897   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.874   0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.053  -0.220   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.053   1.760   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.104   2.104   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.874   3.437   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.564   2.104   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0      -1.334   3.437   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0       0.206   3.437   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.564   4.771   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.206   6.105   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.564   7.438   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.746   6.105   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.746   3.437   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.516   4.771   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.516   2.104   0.000  0.00  0.00           C+0
HETATM   25  H   UNK     0       3.286   3.437   0.000  0.00  0.00           H+0
HETATM   26  C   UNK     0       4.056   2.104   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.826   0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   27                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5   24                                                  
CONECT    5    4    6   15                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    6   10                                                       
CONECT   10    9   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    5   16   17                                             
CONECT   16   15                                                            
CONECT   17   15   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   17   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22    4   25   26                                             
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26    2                                                       
MASTER        0    0    0    0    0    0    0    0   27    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₃₀O₃

Average Mass

342.4790 Da

Monoisotopic Mass

342.21949 Da

IUPAC Name

(3S,3aR,4S,5R,5aR,8S)-3-hydroxy-2,2,5,8-tetramethyl-1,2,3,3a,4,5,5a,6,7,8-decahydropyren-4-yl acetate

Traditional Name

(3S,3aR,4S,5R,5aR,8S)-3-hydroxy-2,2,5,8-tetramethyl-3,3a,4,5,5a,6,7,8-octahydro-1H-pyren-4-yl acetate

CAS Registry Number

Not Available

SMILES

[H][C@]12CC[C@H](C)C3=C1C1=C(CC(C)(C)[C@@H](O)[C@]1([H])[C@@H](OC(C)=O)[C@@H]2C)C=C3

InChI Identifier

InChI=1S/C22H30O3/c1-11-6-8-16-12(2)20(25-13(3)23)19-17-14(7-9-15(11)18(16)17)10-22(4,5)21(19)24/h7,9,11-12,16,19-21,24H,6,8,10H2,1-5H3/t11-,12+,16+,19-,20-,21-/m0/s1

InChI Key

ZLOCFCOPSPEISD-VEWXLAPWSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D_DEPT NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-05-02	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
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, 500 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, 500.133088507, 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
Sinularia 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
Phenanthrol
Phenanthrene
Fatty alcohol ester
Tetralin
Benzenoid
Secondary alcohol
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic homopolycyclic compound

Molecular Framework

Aromatic 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	4.17	ChemAxon
pKa (Strongest Acidic)	14.31	ChemAxon
pKa (Strongest Basic)	-3.1	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	2	ChemAxon
Refractivity	98.52 m³·mol⁻¹	ChemAxon
Polarizability	39.72 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 ]
DOI: 10.1016/j.phytochem.2023.113960
PII: s003194222300376x

Showing NP-Card for Sinucycloamtin C (NP0332360)

MOL for NP0332360 (Sinucycloamtin C)

3D MOL for NP0332360 (Sinucycloamtin C)

3D SDF for NP0332360 (Sinucycloamtin C)

3D-SDF for NP0332360 (Sinucycloamtin C)

PDB for NP0332360 (Sinucycloamtin C)

3D PDB for NP0332360 (Sinucycloamtin C)

SMILES for NP0332360 (Sinucycloamtin C)

INCHI for NP0332360 (Sinucycloamtin C)

Structure for NP0332360 (Sinucycloamtin C)

3D Structure for NP0332360 (Sinucycloamtin C)