NP-MRD: Showing NP-Card for (1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one (NP0257713)

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Record Information

Version

2.0

Created at

2022-09-07 22:55:05 UTC

Updated at

2022-09-07 22:55:05 UTC

NP-MRD ID

NP0257713

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one

Description

Clionamine B belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton. (1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one is found in Cliona celata. Based on a literature review very few articles have been published on Clionamine B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082200552D          

 31 35  0  0  1  0            999 V2000
    1.0649   -4.2611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6749   -3.7056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4988   -2.8996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4609   -3.9561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0709   -3.4006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 31 29  1  1  0  0  0
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  7 31  1  0  0  0  0
M  END

     RDKit          3D

 76 80  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652309082200552D          

 31 35  0  0  1  0            999 V2000
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  7 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0257713

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CCC[C@]1(O)[C@H]2[C@H](C[C@H]3[C@@H]4CCC5C[C@@H](N)CC[C@]5(C)[C@H]4CC[C@]23C)OC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H45NO3/c1-16(2)6-5-11-27(30)23-22(31-24(27)29)15-21-19-8-7-17-14-18(28)9-12-25(17,3)20(19)10-13-26(21,23)4/h16-23,30H,5-15,28H2,1-4H3/t17?,18-,19+,20-,21-,22-,23-,25-,26-,27-/m0/s1

> <INCHI_KEY>
PLLJOGIAOGXLFM-IBODIHDZSA-N

> <FORMULA>
C27H45NO3

> <MOLECULAR_WEIGHT>
431.661

> <EXACT_MASS>
431.339944313

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
52.14700124562815

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,4S,7S,8R,9S,12S,13S,16S)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-one

> <JCHEM_LOGP>
4.700018099129491

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.089625878094727

> <JCHEM_PKA_STRONGEST_BASIC>
10.435470388229042

> <JCHEM_POLAR_SURFACE_AREA>
72.55

> <JCHEM_REFRACTIVITY>
122.67079999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,4S,7S,8R,9S,12S,13S,16S)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       1.988  -7.954   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.126  -6.917   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.798  -5.413   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.594  -7.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.732  -6.348   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.200  -6.815   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.338  -5.779   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       9.250  -7.019   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.188  -4.755   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.684  -5.083   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       7.806  -3.344   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       9.339  -3.497   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.668  -2.719   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.818  -3.743   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.349  -3.573   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.968  -2.163   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      15.498  -1.993   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      16.410  -3.234   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      17.941  -3.065   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      18.853  -4.305   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      20.384  -4.136   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      18.235  -5.716   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      16.704  -5.885   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      15.792  -4.645   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      15.173  -6.055   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      14.261  -4.814   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.643  -6.225   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.112  -6.394   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.200  -5.153   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.438  -6.491   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.668  -5.001   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   31                                             
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   31                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   29                                                  
CONECT   15   14   16   26                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   24                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   18   25   26                                             
CONECT   25   24                                                            
CONECT   26   24   15   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   14   30   31                                             
CONECT   30   29                                                            
CONECT   31   29   12    7                                                  
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₅NO₃

Average Mass

431.6610 Da

Monoisotopic Mass

431.33994 Da

IUPAC Name

(1R,2S,4S,7S,8R,9S,12S,13S,16S)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-one

Traditional Name

(1R,2S,4S,7S,8R,9S,12S,13S,16S)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-one

CAS Registry Number

Not Available

SMILES

CC(C)CCC[C@]1(O)[C@H]2[C@H](C[C@H]3[C@@H]4CCC5C[C@@H](N)CC[C@]5(C)[C@H]4CC[C@]23C)OC1=O

InChI Identifier

InChI=1S/C27H45NO3/c1-16(2)6-5-11-27(30)23-22(31-24(27)29)15-21-19-8-7-17-14-18(28)9-12-25(17,3)20(19)10-13-26(21,23)4/h16-23,30H,5-15,28H2,1-4H3/t17?,18-,19+,20-,21-,22-,23-,25-,26-,27-/m0/s1

InChI Key

PLLJOGIAOGXLFM-IBODIHDZSA-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

Species Name	Source	Reference
Cliona celata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Steroid lactones

Alternative Parents

Substituents

Steroid lactone
20-hydroxysteroid
Hydroxysteroid
Gamma butyrolactone
Oxolane
Tertiary alcohol
Amino acid or derivatives
Carboxylic acid ester
Lactone
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Amine
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Alcohol
Primary amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	4.7	ChemAxon
pKa (Strongest Acidic)	12.09	ChemAxon
pKa (Strongest Basic)	10.44	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	72.55 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	122.67 m³·mol⁻¹	ChemAxon
Polarizability	52.15 Å³	ChemAxon
Number of Rings	5	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

57641768

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102520497

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one (NP0257713)

MOL for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

3D MOL for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

3D SDF for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

3D-SDF for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

PDB for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

3D PDB for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

SMILES for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

INCHI for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

Structure for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)

3D Structure for NP0257713 ((1r,2s,4s,7s,8r,9s,12s,13s,16s)-16-amino-7-hydroxy-9,13-dimethyl-7-(4-methylpentyl)-5-oxapentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosan-6-one)