NP-MRD: Showing NP-Card for Psilostachyin B (NP0064256)

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Record Information

Version

2.0

Created at

2022-04-28 08:31:22 UTC

Updated at

2022-04-28 08:31:22 UTC

NP-MRD ID

NP0064256

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Psilostachyin B

Description

Psilostachyin B belongs to the class of organic compounds known as ambrosanolides and secoambrosanolides. These are sesquiterpene lactones from the Ambrosia family, with a backbone derivative of azuleno[6,5-b]furan-2-one (ambrosanolides) or azuleno[4,5-b]furan-2-one (secoambrosanolides). Psilostachyin B is found in Ambrosia artemisiifolia, Ambrosia confertiflora, Ambrosia peruviana, Ambrosia psilostachya and Ambrosia tenuifolia. Psilostachyin B was first documented in 2005 (PMID: 16254826). Based on a literature review very few articles have been published on Psilostachyin B (PMID: 29148613).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 39  0  0  0  0  0  0  0  0999 V2000
    3.9879    0.1455   -0.5299 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9742    0.6410    0.1312 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7584    2.0384    0.4557 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6294    2.9769    0.4887 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4001    2.1592    0.7278 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7637    0.8942    0.7624 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8322   -0.1098    0.6899 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5289   -1.3931    0.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3555   -2.0292    0.7065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9549   -1.4752    0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0868   -2.4054    0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2279   -0.2533   -0.1464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6258   -0.0214   -0.4787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1949    1.2198    0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1860    2.2640    0.3754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4635    3.2955    1.0307 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9582    2.1373   -0.1821 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2632    0.8844   -0.3271 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3159    0.9040   -1.7122 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7986    0.7458   -0.9167 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0280   -0.9179   -0.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2208    0.8420    1.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1341   -0.3679    1.7510 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4071   -2.0800    0.2119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4147   -1.3669   -1.0652 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3486   -3.1115    0.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5061   -2.0329    1.7965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8428   -2.1392    1.1482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5525   -2.6401   -0.6234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7230   -3.4216    0.7122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6735    0.2425   -1.5711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3422   -0.8045   -0.2925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5073    0.8881    1.2449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0757    1.5343   -0.3678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0195    1.7942   -2.3236 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4118    0.9315   -1.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1185    0.0316   -2.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  1  6
 18  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  2  3
  2  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 18 12  1  0
  7  6  1  0
 11 28  1  0
 11 29  1  0
 11 30  1  0
 13 31  1  0
 13 32  1  0
 14 33  1  0
 14 34  1  0
 19 35  1  0
 19 36  1  0
 19 37  1  0
  6 22  1  1
  1 20  1  0
  1 21  1  0
  7 23  1  1
  8 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
M  END


  Mrv1652304282210312D          

 19 21  0  0  1  0            999 V2000
    2.9712    3.3533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1860    2.5567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6972    1.8921    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8728    1.8599    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3337    2.4844    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4857    3.2952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2145    3.6819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5732    2.1646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1326    2.5918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6423    1.3425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0179    0.8033    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4456    1.1542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0283    1.1365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8483    1.0455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1795    0.2899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3371    1.7101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0060    2.4657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2594    1.1929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5956    3.8924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  5  8  1  6  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  4 12  1  6  0  0  0
  3 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
  2 17  1  0  0  0  0
  3 18  1  6  0  0  0
  1 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0064256

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C2CCC(=O)O[C@@]2(C)[C@@H]2OC(=O)C(=C)[C@@H]2CC1

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O4/c1-8-4-5-10-9(2)14(17)18-13(10)15(3)11(8)6-7-12(16)19-15/h10,13H,2,4-7H2,1,3H3/t10-,13+,15+/m0/s1

> <INCHI_KEY>
IOGFBFUSBVLQMS-PSOPSSQASA-N

> <FORMULA>
C15H18O4

> <MOLECULAR_WEIGHT>
262.305

> <EXACT_MASS>
262.12050906

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.139456649370505

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,6S)-1,9-dimethyl-5-methylidene-3,14-dioxatricyclo[8.4.0.0^{2,6}]tetradec-9-ene-4,13-dione

> <ALOGPS_LOGP>
2.31

> <JCHEM_LOGP>
2.2834220593333336

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.658538125434014

> <JCHEM_POLAR_SURFACE_AREA>
52.6

> <JCHEM_REFRACTIVITY>
68.4017

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.90e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,6S)-1,9-dimethyl-5-methylidene-3,14-dioxatricyclo[8.4.0.0^{2,6}]tetradec-9-ene-4,13-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       5.546   6.259   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.947   4.773   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.035   3.532   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.496   3.472   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.490   4.638   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.773   6.151   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.134   6.873   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.070   4.041   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.247   4.838   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.199   2.506   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.033   1.500   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.698   2.155   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       5.653   2.121   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.184   1.952   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.802   0.541   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.096   3.192   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.478   4.603   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.218   2.227   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.712   7.266   0.000  0.00  0.00           C+0
CONECT    1    2    7   19                                                  
CONECT    2    1    3   17                                                  
CONECT    3    2    4   13   18                                             
CONECT    4    3    5   12                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    1                                                       
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    4                                                       
CONECT   13    3   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16    2                                                       
CONECT   18    3                                                            
CONECT   19    1                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₈O₄

Average Mass

262.3050 Da

Monoisotopic Mass

262.12051 Da

IUPAC Name

(1R,2R,6S)-1,9-dimethyl-5-methylidene-3,14-dioxatricyclo[8.4.0.0^{2,6}]tetradec-9-ene-4,13-dione

Traditional Name

(1R,2R,6S)-1,9-dimethyl-5-methylidene-3,14-dioxatricyclo[8.4.0.0^{2,6}]tetradec-9-ene-4,13-dione

CAS Registry Number

Not Available

SMILES

CC1=C2CCC(=O)O[C@@]2(C)[C@@H]2OC(=O)C(=C)[C@@H]2CC1

InChI Identifier

InChI=1S/C15H18O4/c1-8-4-5-10-9(2)14(17)18-13(10)15(3)11(8)6-7-12(16)19-15/h10,13H,2,4-7H2,1,3H3/t10-,13+,15+/m0/s1

InChI Key

IOGFBFUSBVLQMS-PSOPSSQASA-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
Ambrosia artemisiifolia	Plant	KNApSAcK
Ambrosia confertiflora	LOTUS Database	35616633
Ambrosia peruviana	LOTUS Database	35616633
Ambrosia psilostachya	Plant	KNApSAcK
Ambrosia tenuifolia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ambrosanolides and secoambrosanolides. These are sesquiterpene lactones from the Ambrosia family, with a backbone derivative of azuleno[6,5-b]furan-2-one (ambrosanolides) or azuleno[4,5-b]furan-2-one (secoambrosanolides).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Ambrosanolides and secoambrosanolides

Alternative Parents

Substituents

Secoambrosanolide
Sesquiterpenoid
Delta valerolactone
Delta_valerolactone
Dicarboxylic acid or derivatives
Gamma butyrolactone
Oxane
Alpha,beta-unsaturated carboxylic ester
Oxolane
Enoate ester
Lactone
Carboxylic acid ester
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
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	2.31	ALOGPS
logP	2.28	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Basic)	-6.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	52.6 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	68.4 m³·mol⁻¹	ChemAxon
Polarizability	27.14 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

C00021197

Chemspider ID

4478756

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5320768

PDB ID

Not Available

ChEBI ID

182461

Good Scents ID

Not Available

References

General References

Ding W, Huang R, Zhou Z, He H, Li Y: Ambrosia artemisiifolia as a potential resource for management of golden apple snails, Pomacea canaliculata (Lamarck). Pest Manag Sci. 2018 Apr;74(4):944-949. doi: 10.1002/ps.4792. Epub 2018 Jan 16. [PubMed:29148613 ]
Sturgeon CM, Craig K, Brown C, Rundle NT, Andersen RJ, Roberge M: Modulation of the G2 cell cycle checkpoint by sesquiterpene lactones psilostachyins A and C isolated from the common ragweed Ambrosia artemisiifolia. Planta Med. 2005 Oct;71(10):938-43. doi: 10.1055/s-2005-873109. [PubMed:16254826 ]

Showing NP-Card for Psilostachyin B (NP0064256)

MOL for NP0064256 (Psilostachyin B)

3D MOL for NP0064256 (Psilostachyin B)

3D SDF for NP0064256 (Psilostachyin B)

3D-SDF for NP0064256 (Psilostachyin B)

PDB for NP0064256 (Psilostachyin B)

3D PDB for NP0064256 (Psilostachyin B)

SMILES for NP0064256 (Psilostachyin B)

INCHI for NP0064256 (Psilostachyin B)

Structure for NP0064256 (Psilostachyin B)

3D Structure for NP0064256 (Psilostachyin B)