NP-MRD: Showing NP-Card for (1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol (NP0252819)

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Record Information

Version

2.0

Created at

2022-09-07 16:28:13 UTC

Updated at

2022-09-07 16:28:13 UTC

NP-MRD ID

NP0252819

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol

Description

Certonardosterol N1 belongs to the class of organic compounds known as stigmastanes and derivatives. These are sterol lipids with a structure based on the stigmastane skeleton, which consists of a cholestane moiety bearing an ethyl group at the carbon atom C24. (1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol is found in Certonardoa semiregularis. Based on a literature review very few articles have been published on Certonardosterol N1.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072218282D          

 34 37  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072218282D          

 34 37  0  0  1  0            999 V2000
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   16.8783   -3.4534    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5193   -3.8949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7123   -3.7234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4574   -2.9388    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.9053   -3.5519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6504   -2.7673    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.0984   -3.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2914   -3.2088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0365   -2.4242    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.4234   -2.9762    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
  4  5  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 12 10  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  1  0  0  0
 17 15  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  1  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 18 30  1  0  0  0  0
 30 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 17 33  1  0  0  0  0
 12 33  1  0  0  0  0
 33 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0252819

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H](CCO)CC[C@@H](C)[C@H]1[C@@H](O)[C@@H](O)[C@H]2[C@@H]3C[C@H](O)[C@H]4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C29H52O5/c1-16(2)18(10-13-30)7-6-17(3)24-26(33)27(34)25-20-15-23(32)22-14-19(31)8-11-28(22,4)21(20)9-12-29(24,25)5/h16-27,30-34H,6-15H2,1-5H3/t17-,18-,19+,20-,21+,22-,23+,24+,25-,26-,27+,28-,29-/m1/s1

> <INCHI_KEY>
CQDRJWAYTUMGAI-OJGOSNDTSA-N

> <FORMULA>
C29H52O5

> <MOLECULAR_WEIGHT>
480.73

> <EXACT_MASS>
480.381474774

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
86

> <JCHEM_AVERAGE_POLARIZABILITY>
57.76744778054041

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,5S,7S,8S,10R,11S,12S,13R,14R,15R)-14-[(2R,5R)-7-hydroxy-5-(propan-2-yl)heptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8,12,13-tetrol

> <JCHEM_LOGP>
3.198898185666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.602441351287212

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.596188440966756

> <JCHEM_PKA_STRONGEST_BASIC>
-1.8853422373639237

> <JCHEM_POLAR_SURFACE_AREA>
101.15

> <JCHEM_REFRACTIVITY>
135.3143

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5S,7S,8S,10R,11S,12S,13R,14R,15R)-14-[(2R,5R)-7-hydroxy-5-isopropylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8,12,13-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      17.060  -1.589   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.726  -2.359   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.393  -1.589   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.726  -3.899   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.393  -4.669   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.059  -3.899   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.725  -4.669   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      17.060  -4.669   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.394  -3.899   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.728  -4.669   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.728  -6.209   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      21.061  -3.899   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.222  -2.367   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      20.078  -1.337   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      22.729  -2.047   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      23.355  -0.640   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      23.499  -3.381   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      25.005  -3.701   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      26.035  -2.556   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      27.542  -2.877   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      28.572  -1.732   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      28.018  -4.341   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      29.524  -4.661   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      30.000  -6.126   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      31.506  -6.446   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      28.969  -7.271   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      27.463  -6.950   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      26.987  -5.486   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      25.957  -6.630   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      25.481  -5.166   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      24.450  -6.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      22.944  -5.990   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      22.468  -4.525   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      21.324  -5.556   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    4    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   33                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   33                                                  
CONECT   18   17   19   30                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   22   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   18   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   17   12   34                                             
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₅₂O₅

Average Mass

480.7300 Da

Monoisotopic Mass

480.38147 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H](CCO)CC[C@@H](C)[C@H]1[C@@H](O)[C@@H](O)[C@H]2[C@@H]3C[C@H](O)[C@H]4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C

InChI Identifier

InChI=1S/C29H52O5/c1-16(2)18(10-13-30)7-6-17(3)24-26(33)27(34)25-20-15-23(32)22-14-19(31)8-11-28(22,4)21(20)9-12-29(24,25)5/h16-27,30-34H,6-15H2,1-5H3/t17-,18-,19+,20-,21+,22-,23+,24+,25-,26-,27+,28-,29-/m1/s1

InChI Key

CQDRJWAYTUMGAI-OJGOSNDTSA-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
Certonardoa semiregularis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stigmastanes and derivatives. These are sterol lipids with a structure based on the stigmastane skeleton, which consists of a cholestane moiety bearing an ethyl group at the carbon atom C24.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Stigmastanes and derivatives

Direct Parent

Stigmastanes and derivatives

Alternative Parents

Substituents

C24-propyl-sterol-skeleton
Triterpenoid
Stigmastane-skeleton
3-hydroxysteroid
6-hydroxysteroid
3-beta-hydroxysteroid
16-hydroxysteroid
16-beta-hydroxysteroid
15-hydroxysteroid
Hydroxysteroid
Fatty alcohol
Fatty acyl
Cyclic alcohol
Secondary alcohol
Polyol
Organooxygen compound
Primary alcohol
Organic oxygen compound
Hydrocarbon derivative
Alcohol
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

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

9606470

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11431595

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol (NP0252819)

MOL for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

3D MOL for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

3D SDF for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

3D-SDF for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

PDB for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

3D PDB for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

SMILES for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

INCHI for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

Structure for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)

3D Structure for NP0252819 ((1r,2r,3s,3as,3br,5s,5as,7s,9ar,9bs,11ar)-1-[(2r,5r)-7-hydroxy-5-isopropylheptan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-2,3,5,7-tetrol)