NP-MRD: Showing NP-Card for Pachystermine B (NP0084310)

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Record Information

Version

2.0

Created at

2022-04-29 05:04:53 UTC

Updated at

2022-04-29 05:04:54 UTC

NP-MRD ID

NP0084310

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pachystermine B

Description

Pachystermine B belongs to the class of organic compounds known as hydroxysteroids. Hydroxysteroids are compounds containing an steroid backbone, with at least one hydrogen substituted by a hydroxyl group. Pachystermine B is found in Pachysandra terminalis. Based on a literature review very few articles have been published on Pachystermine B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207042D          

 39 43  0  0  1  0            999 V2000
    2.2580   -2.3340    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1731   -1.7404    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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  2  1  1  6  0  0  0
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  2 38  1  0  0  0  0
 38 39  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292207042D          

 39 43  0  0  1  0            999 V2000
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    8.4852   -2.4209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6731   -2.5662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8610   -2.7114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3292   -2.0807    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0489   -2.8566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5171   -2.2259    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7974   -1.4499    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2368   -3.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4247   -3.1470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8928   -2.5163    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5330   -3.2587    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  1  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  2  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
 10 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 23 27  1  0  0  0  0
 21 27  1  0  0  0  0
 27 28  2  0  0  0  0
 20 29  1  6  0  0  0
 20 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 16 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  0  0  0  0
 12 34  1  0  0  0  0
 34 35  1  6  0  0  0
 34 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 10 38  1  0  0  0  0
  2 38  1  0  0  0  0
 38 39  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0084310

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@]4([H])[C@@H](O)[C@]([H])(CC[C@]4(C)[C@@]3([H])CC[C@]12C)N1C[C@@H](C(C)C)C1=O)[C@H](C)N(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C29H50N2O2/c1-17(2)20-16-31(27(20)33)25-13-15-29(5)23-12-14-28(4)21(18(3)30(6)7)10-11-22(28)19(23)8-9-24(29)26(25)32/h17-26,32H,8-16H2,1-7H3/t18-,19-,20-,21+,22-,23-,24-,25-,26+,28+,29+/m0/s1

> <INCHI_KEY>
AENZWKGHCPXWBZ-APKZJJHSSA-N

> <FORMULA>
C29H50N2O2

> <MOLECULAR_WEIGHT>
458.731

> <EXACT_MASS>
458.387228858

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
83

> <JCHEM_AVERAGE_POLARIZABILITY>
57.2213476039596

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-1-[(1S,2R,5S,6R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-6-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]-3-(propan-2-yl)azetidin-2-one

> <ALOGPS_LOGP>
4.45

> <JCHEM_LOGP>
4.639790460333334

> <ALOGPS_LOGS>
-4.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.307185058198929

> <JCHEM_PKA_STRONGEST_BASIC>
10.300254239778164

> <JCHEM_POLAR_SURFACE_AREA>
43.78

> <JCHEM_REFRACTIVITY>
134.80849999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.70e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-1-[(1S,2R,5S,6R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-6-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]-3-isopropylazetidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  H   UNK     0       4.215  -4.357   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.257  -5.652   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       2.312  -6.868   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.676  -4.226   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM   11  H   UNK     0       8.783  -4.426   0.000  0.00  0.00           H+0
HETATM   12  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0       8.313  -1.800   0.000  0.00  0.00           H+0
HETATM   14  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   17  H   UNK     0      13.330  -3.613   0.000  0.00  0.00           H+0
HETATM   18  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      14.377  -0.716   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      16.362  -3.071   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      17.243  -1.807   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      18.506  -2.687   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      20.022  -2.416   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      20.545  -0.968   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      21.015  -3.594   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      17.626  -3.951   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      17.897  -5.467   0.000  0.00  0.00           O+0
HETATM   29  H   UNK     0      15.839  -4.519   0.000  0.00  0.00           H+0
HETATM   30  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   35  H   UNK     0      10.822  -2.707   0.000  0.00  0.00           H+0
HETATM   36  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8   38                                             
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    2    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12   38                                             
CONECT   11   10                                                            
CONECT   12   10   13   14   34                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   32                                             
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   29   30                                             
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   27                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   23   21   28                                                  
CONECT   28   27                                                            
CONECT   29   20                                                            
CONECT   30   20   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   16   33   34                                             
CONECT   33   32                                                            
CONECT   34   32   12   35   36                                             
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   10    2   39                                             
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₅₀N₂O₂

Average Mass

458.7310 Da

Monoisotopic Mass

458.38723 Da

IUPAC Name

(3R)-1-[(1S,2R,5S,6R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-6-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]-3-(propan-2-yl)azetidin-2-one

Traditional Name

(3R)-1-[(1S,2R,5S,6R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-6-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]-3-isopropylazetidin-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@]4([H])[C@@H](O)[C@]([H])(CC[C@]4(C)[C@@]3([H])CC[C@]12C)N1C[C@@H](C(C)C)C1=O)[C@H](C)N(C)C

InChI Identifier

InChI=1S/C29H50N2O2/c1-17(2)20-16-31(27(20)33)25-13-15-29(5)23-12-14-28(4)21(18(3)30(6)7)10-11-22(28)19(23)8-9-24(29)26(25)32/h17-26,32H,8-16H2,1-7H3/t18-,19-,20-,21+,22-,23-,24-,25-,26+,28+,29+/m0/s1

InChI Key

AENZWKGHCPXWBZ-APKZJJHSSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Pachysandra terminalis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxysteroids. Hydroxysteroids are compounds containing an steroid backbone, with at least one hydrogen substituted by a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Hydroxysteroids

Direct Parent

Hydroxysteroids

Alternative Parents

Substituents

22-azasteroid
Pregnane-skeleton
Pregnane-type alkaloid
Steroidal alkaloid
Hydroxysteroid
4-hydroxysteroid
Azasteroid
Monobactam
Alkaloid or derivatives
Beta-lactam
Cyclic alcohol
Tertiary carboxylic acid amide
Amino acid or derivatives
Secondary alcohol
Lactam
Carboxamide group
Tertiary amine
Azetidine
Tertiary aliphatic amine
Carboxylic acid derivative
Organoheterocyclic compound
Azacycle
Alcohol
Organonitrogen compound
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
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	4.45	ALOGPS
logP	4.64	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	14.31	ChemAxon
pKa (Strongest Basic)	10.3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	43.78 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	134.81 m³·mol⁻¹	ChemAxon
Polarizability	57.22 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

C00053621

Chemspider ID

28526486

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70695310

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pachystermine B (NP0084310)

MOL for NP0084310 (Pachystermine B)

3D MOL for NP0084310 (Pachystermine B)

3D SDF for NP0084310 (Pachystermine B)

3D-SDF for NP0084310 (Pachystermine B)

PDB for NP0084310 (Pachystermine B)

3D PDB for NP0084310 (Pachystermine B)

SMILES for NP0084310 (Pachystermine B)

INCHI for NP0084310 (Pachystermine B)

Structure for NP0084310 (Pachystermine B)

3D Structure for NP0084310 (Pachystermine B)