NP-MRD: Showing NP-Card for (1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one (NP0279629)

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Record Information

Version

2.0

Created at

2022-09-09 05:05:23 UTC

Updated at

2022-09-09 05:05:24 UTC

NP-MRD ID

NP0279629

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one

Description

(1S,2S,5S,6S,9S,13S,16S,18R)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]Icos-11-en-8-one belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. (1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one is found in Cucumaria echinata. Based on a literature review very few articles have been published on (1S,2S,5S,6S,9S,13S,16S,18R)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]Icos-11-en-8-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092207052D          

 34 38  0  0  1  0            999 V2000
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M  END

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M  END


  Mrv1652309092207052D          

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    4.5178   -0.3556    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0213    0.3033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579   -1.3162    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9828   -2.0234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0847   -1.9921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2958   -1.7510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2813   -0.9261    0.0000 C   0  0  2  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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 13 11  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 17 16  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 21 24  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
 27 28  1  0  0  0  0
 16 28  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  6  0  0  0
 17 30  1  0  0  0  0
 13 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 34 33  1  6  0  0  0
  8 34  1  0  0  0  0
 13 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0279629

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CC(=O)C[C@]1(C)OC(=O)[C@]23CC=C4[C@@H](CC[C@H]5C(C)(C)[C@@H](O)CC[C@]45C)[C@]2(C)CC[C@H]13

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O4/c1-18(2)16-19(31)17-29(7)23-11-14-28(6)21-8-9-22-26(3,4)24(32)12-13-27(22,5)20(21)10-15-30(23,28)25(33)34-29/h10,18,21-24,32H,8-9,11-17H2,1-7H3/t21-,22+,23-,24+,27-,28+,29+,30-/m1/s1

> <INCHI_KEY>
ATMMDJDROCVXEE-JICQDWDYSA-N

> <FORMULA>
C30H46O4

> <MOLECULAR_WEIGHT>
470.694

> <EXACT_MASS>
470.339609961

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
54.92291488867492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5S,6S,9S,13S,16S,18R)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icos-11-en-8-one

> <JCHEM_LOGP>
5.6735560603333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.5537932339341

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.544141903658048

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8069705296647748

> <JCHEM_POLAR_SURFACE_AREA>
63.60000000000001

> <JCHEM_REFRACTIVITY>
134.35580000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5S,6S,9S,13S,16S,18R)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icos-11-en-8-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.934   1.529   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.772   0.519   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.066  -0.993   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.316   1.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.154   0.010   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.447  -1.502   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.302   0.511   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.465  -0.499   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.339  -1.549   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.348   0.763   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.821   0.313   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.051   1.240   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.848  -1.227   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.449   0.190   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.978   0.378   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.905  -0.852   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.303  -2.269   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.230  -3.499   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.759  -3.311   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.360  -1.894   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.889  -1.706   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.808  -3.244   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.389  -2.052   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.490  -0.288   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      13.019  -0.100   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.563   0.942   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.035   0.754   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.433  -0.664   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.506   0.566   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.775  -2.457   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.568  -3.777   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.892  -3.719   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.419  -3.268   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.392  -1.729   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    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10   34                                             
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   30   34                                             
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   28                                                  
CONECT   17   16   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   16   20   29                                             
CONECT   29   28                                                            
CONECT   30   17   13   31   32                                             
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33    8   13                                                  
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₆O₄

Average Mass

470.6940 Da

Monoisotopic Mass

470.33961 Da

IUPAC Name

(1S,2S,5S,6S,9S,13S,16S,18R)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icos-11-en-8-one

Traditional Name

(1S,2S,5S,6S,9S,13S,16S,18R)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icos-11-en-8-one

CAS Registry Number

Not Available

SMILES

CC(C)CC(=O)C[C@]1(C)OC(=O)[C@]23CC=C4[C@@H](CC[C@H]5C(C)(C)[C@@H](O)CC[C@]45C)[C@]2(C)CC[C@H]13

InChI Identifier

InChI=1S/C30H46O4/c1-18(2)16-19(31)17-29(7)23-11-14-28(6)21-8-9-22-26(3,4)24(32)12-13-27(22,5)20(21)10-15-30(23,28)25(33)34-29/h10,18,21-24,32H,8-9,11-17H2,1-7H3/t21-,22+,23-,24+,27-,28+,29+,30-/m1/s1

InChI Key

ATMMDJDROCVXEE-JICQDWDYSA-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
Cucumaria echinata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Hydroxy bile acid, alcohol, or derivatives
Monohydroxy bile acid, alcohol, or derivatives
Bile acid, alcohol, or derivatives
Steroid lactone
3-hydroxysteroid
3-beta-hydroxysteroid
Hydroxysteroid
Steroid
Gamma butyrolactone
Cyclic alcohol
Tetrahydrofuran
Carboxylic acid ester
Secondary alcohol
Ketone
Lactone
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic oxide
Organooxygen compound
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	5.67	ChemAxon
pKa (Strongest Acidic)	18.54	ChemAxon
pKa (Strongest Basic)	-0.81	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	134.36 m³·mol⁻¹	ChemAxon
Polarizability	54.92 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

10244881

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14467309

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one (NP0279629)

MOL for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

3D MOL for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

3D SDF for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

3D-SDF for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

PDB for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

3D PDB for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

SMILES for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

INCHI for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

Structure for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)

3D Structure for NP0279629 ((1s,2s,5s,6s,9s,13s,16s,18r)-16-hydroxy-2,6,13,17,17-pentamethyl-6-(4-methyl-2-oxopentyl)-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icos-11-en-8-one)