NP-MRD: Showing NP-Card for Sinucycloamtin D (NP0332356)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2024-01-11 16:00:35 UTC

Updated at

2024-09-03 04:18:56 UTC

NP-MRD ID

NP0332356

DOI

https://doi.org/10.57994/1571

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sinucycloamtin D

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01112416002D          

 24 27  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
    0.9355    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
 17 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21  4  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
  2 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332356

> <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](O)[C@@H]2C)C=C3

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O2/c1-10-5-7-14-11(2)18(21)17-15-12(6-8-13(10)16(14)15)9-20(3,4)19(17)22/h6,8,10-11,14,17-19,21-22H,5,7,9H2,1-4H3/t10-,11+,14+,17-,18-,19-/m0/s1

> <INCHI_KEY>
BDNQNDPWUBCZSS-PIMJOXQRSA-N

> <FORMULA>
C20H28O2

> <MOLECULAR_WEIGHT>
300.442

> <EXACT_MASS>
300.208930142

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
35.601616374350876

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,6S,8aR,9R,10S,10aS)-2,2,6,9-tetramethyl-1,2,3,6,7,8,8a,9,10,10a-decahydropyrene-1,10-diol

> <JCHEM_LOGP>
3.729105519999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.812024049478849

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.098809237813207

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0144955718267283

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
89.37049999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,6S,8aR,9R,10S,10aS)-2,2,6,9-tetramethyl-3,6,7,8,8a,9,10,10a-octahydro-1H-pyrene-1,10-diol

> <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       1.746   3.437   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.516   4.771   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.516   2.104   0.000  0.00  0.00           C+0
HETATM   22  H   UNK     0       3.286   3.437   0.000  0.00  0.00           H+0
HETATM   23  C   UNK     0       4.056   2.104   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.826   0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   24                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5   21                                                  
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   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19    4   22   23                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23    2                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₈O₂

Average Mass

300.4420 Da

Monoisotopic Mass

300.20893 Da

IUPAC Name

(1S,6S,8aR,9R,10S,10aS)-2,2,6,9-tetramethyl-1,2,3,6,7,8,8a,9,10,10a-decahydropyrene-1,10-diol

Traditional Name

(1S,6S,8aR,9R,10S,10aS)-2,2,6,9-tetramethyl-3,6,7,8,8a,9,10,10a-octahydro-1H-pyrene-1,10-diol

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](O)[C@@H]2C)C=C3

InChI Identifier

InChI=1S/C20H28O2/c1-10-5-7-14-11(2)18(21)17-15-12(6-8-13(10)16(14)15)9-20(3,4)19(17)22/h6,8,10-11,14,17-19,21-22H,5,7,9H2,1-4H3/t10-,11+,14+,17-,18-,19-/m0/s1

InChI Key

BDNQNDPWUBCZSS-PIMJOXQRSA-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
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 126 MHz, CDCl3, experimental)	simmswli@163.com	School of Medicine Shanghai University	Song-Wei Li	2024-01-11	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 599.6337058, 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

Classification

Not classified

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	3.73	ChemAxon
pKa (Strongest Acidic)	14.1	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	89.37 m³·mol⁻¹	ChemAxon
Polarizability	35.6 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

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 Sinucycloamtin D (NP0332356)

MOL for NP0332356 (Sinucycloamtin D)

3D MOL for NP0332356 (Sinucycloamtin D)

3D SDF for NP0332356 (Sinucycloamtin D)

3D-SDF for NP0332356 (Sinucycloamtin D)

PDB for NP0332356 (Sinucycloamtin D)

3D PDB for NP0332356 (Sinucycloamtin D)

SMILES for NP0332356 (Sinucycloamtin D)

INCHI for NP0332356 (Sinucycloamtin D)

Structure for NP0332356 (Sinucycloamtin D)

3D Structure for NP0332356 (Sinucycloamtin D)