NP-MRD: Showing NP-Card for Pachanol B (NP0083163)

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Record Information

Version

2.0

Created at

2022-04-29 04:12:02 UTC

Updated at

2022-04-29 04:12:02 UTC

NP-MRD ID

NP0083163

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pachanol B

Description

(1S,3S,4R,5S,8R,10R,13S,14R,20S,21R)-10-hydroxy-20-(hydroxymethyl)-3,5,9,9,13,20-hexamethyl-22-oxahexacyclo[19.2.1.0¹,¹⁸.0⁴,¹⁷.0⁵,¹⁴.0⁸,¹³]Tetracosa-15,17-dien-23-one belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. Pachanol B is found in Trichoereus pachanoi. Based on a literature review very few articles have been published on (1S,3S,4R,5S,8R,10R,13S,14R,20S,21R)-10-hydroxy-20-(hydroxymethyl)-3,5,9,9,13,20-hexamethyl-22-oxahexacyclo[19.2.1.0¹,¹⁸.0⁴,¹⁷.0⁵,¹⁴.0⁸,¹³]Tetracosa-15,17-dien-23-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292206122D          

 34 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292206122D          

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  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  6  0  0  0
  8 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  1  0  0  0
 14 18  1  6  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 13 21  1  0  0  0  0
 20 22  1  6  0  0  0
 22 23  1  0  0  0  0
 20 24  1  1  0  0  0
 19 25  1  0  0  0  0
 25 26  1  0  0  0  0
 14 26  1  0  0  0  0
 26 27  2  0  0  0  0
 12 28  1  0  0  0  0
 28 29  2  0  0  0  0
  7 29  1  6  0  0  0
  8 30  1  1  0  0  0
  5 31  1  6  0  0  0
  3 32  1  0  0  0  0
  3 33  1  0  0  0  0
  2 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0083163

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C[C@@]23C[C@@H](OC2=O)[C@](C)(CO)CC3=C2C=C[C@@H]3[C@@]4(C)CC[C@@H](O)C(C)(C)[C@@H]4CC[C@]3(C)[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C30H44O4/c1-17-13-30-15-23(34-25(30)33)27(4,16-31)14-19(30)18-7-8-21-28(5)12-10-22(32)26(2,3)20(28)9-11-29(21,6)24(17)18/h7-8,17,20-24,31-32H,9-16H2,1-6H3/t17-,20-,21+,22+,23+,24-,27-,28-,29-,30-/m0/s1

> <INCHI_KEY>
NPXRQQCHKINHAI-RLUBVRRYSA-N

> <FORMULA>
C30H44O4

> <MOLECULAR_WEIGHT>
468.678

> <EXACT_MASS>
468.323959897

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
53.917559704583496

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3S,4R,5S,8R,10R,13S,14R,20S,21R)-10-hydroxy-20-(hydroxymethyl)-3,5,9,9,13,20-hexamethyl-22-oxahexacyclo[19.2.1.0^{1,18}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosa-15,17-dien-23-one

> <ALOGPS_LOGP>
4.04

> <JCHEM_LOGP>
4.329114829333334

> <ALOGPS_LOGS>
-5.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.489420328730784

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.02803449689737

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8351273483901284

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
134.34599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.06e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3S,4R,5S,8R,10R,13S,14R,20S,21R)-10-hydroxy-20-(hydroxymethyl)-3,5,9,9,13,20-hexamethyl-22-oxahexacyclo[19.2.1.0^{1,18}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosa-15,17-dien-23-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  C   UNK     0      10.637   2.767   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.244   1.351   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.321   0.118   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.792   0.301   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.185   1.716   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.108   2.949   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.656   1.899   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.734   0.666   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.340  -0.750   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.869  -0.932   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.205   0.848   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.598   2.263   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.036   2.488   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.043   1.163   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.755  -0.242   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.289  -0.404   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.913  -1.812   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.062   2.065   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.095   2.824   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.175   4.151   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.425   4.012   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.408   5.074   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.226   6.603   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.098   5.689   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -1.660   1.315   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -0.391   0.303   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.494  -1.234   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       4.520   3.497   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.050   3.314   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.811  -0.568   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.579   3.132   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.521  -0.847   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      10.192  -1.416   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      12.773   1.169   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   34                                                  
CONECT    3    2    4   32   33                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   31                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   29                                                  
CONECT    8    7    9   11   30                                             
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   16                                                  
CONECT   12   11   13   28                                                  
CONECT   13   12   14   21                                                  
CONECT   14   13   15   18   26                                             
CONECT   15   14   16                                                       
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
CONECT   18   14   19                                                       
CONECT   19   18   20   25                                                  
CONECT   20   19   21   22   24                                             
CONECT   21   20   13                                                       
CONECT   22   20   23                                                       
CONECT   23   22                                                            
CONECT   24   20                                                            
CONECT   25   19   26                                                       
CONECT   26   25   14   27                                                  
CONECT   27   26                                                            
CONECT   28   12   29                                                       
CONECT   29   28    7                                                       
CONECT   30    8                                                            
CONECT   31    5                                                            
CONECT   32    3                                                            
CONECT   33    3                                                            
CONECT   34    2                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₄O₄

Average Mass

468.6780 Da

Monoisotopic Mass

468.32396 Da

IUPAC Name

(1S,3S,4R,5S,8R,10R,13S,14R,20S,21R)-10-hydroxy-20-(hydroxymethyl)-3,5,9,9,13,20-hexamethyl-22-oxahexacyclo[19.2.1.0^{1,18}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosa-15,17-dien-23-one

Traditional Name

(1S,3S,4R,5S,8R,10R,13S,14R,20S,21R)-10-hydroxy-20-(hydroxymethyl)-3,5,9,9,13,20-hexamethyl-22-oxahexacyclo[19.2.1.0^{1,18}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosa-15,17-dien-23-one

CAS Registry Number

Not Available

SMILES

C[C@H]1C[C@@]23C[C@@H](OC2=O)[C@](C)(CO)CC3=C2C=C[C@@H]3[C@@]4(C)CC[C@@H](O)C(C)(C)[C@@H]4CC[C@]3(C)[C@@H]12

InChI Identifier

InChI=1S/C30H44O4/c1-17-13-30-15-23(34-25(30)33)27(4,16-31)14-19(30)18-7-8-21-28(5)12-10-22(32)26(2,3)20(28)9-11-29(21,6)24(17)18/h7-8,17,20-24,31-32H,9-16H2,1-6H3/t17-,20-,21+,22+,23+,24-,27-,28-,29-,30-/m0/s1

InChI Key

NPXRQQCHKINHAI-RLUBVRRYSA-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
Trichoereus pachanoi	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Gamma butyrolactones

Direct Parent

Gamma butyrolactones

Alternative Parents

Substituents

Oxepane
Gamma butyrolactone
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
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	4.04	ALOGPS
logP	4.33	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	15.03	ChemAxon
pKa (Strongest Basic)	-0.84	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	134.35 m³·mol⁻¹	ChemAxon
Polarizability	53.92 Å³	ChemAxon
Number of Rings	6	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163105251

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pachanol B (NP0083163)

MOL for NP0083163 (Pachanol B)

3D MOL for NP0083163 (Pachanol B)

3D SDF for NP0083163 (Pachanol B)

3D-SDF for NP0083163 (Pachanol B)

PDB for NP0083163 (Pachanol B)

3D PDB for NP0083163 (Pachanol B)

SMILES for NP0083163 (Pachanol B)

INCHI for NP0083163 (Pachanol B)

Structure for NP0083163 (Pachanol B)

3D Structure for NP0083163 (Pachanol B)