NP-MRD: Showing NP-Card for Pungiolide B (NP0064060)

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Record Information

Version

2.0

Created at

2022-04-28 08:21:18 UTC

Updated at

2022-04-28 08:21:18 UTC

NP-MRD ID

NP0064060

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pungiolide B

Description

CHEMBL2380791 belongs to the class of organic compounds known as xanthanolides. These are sesquiterpenoids with a structure based on the xanthanolide skeleton consistsing of a cycloheptane ring usually attached to a four-carbon chain (at carbon 1 ) and a methyl group (at carbon 10), and fused to a five-member lactone ring (sharing carbons 7 and 8). The lactone ring can be conjugated with a methyl or methylene group at position 11. Pungiolide B is found in Xanthium pungens and Xanthium strumarium. Based on a literature review very few articles have been published on CHEMBL2380791.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282210212D          

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M  END

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  5 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  9 15  1  1  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 18 17  1  6  0  0  0
 18 19  1  0  0  0  0
  9 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 18 24  1  0  0  0  0
 23 25  1  6  0  0  0
 22 26  1  0  0  0  0
 21 26  1  1  0  0  0
 22 27  1  6  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
  5 32  1  1  0  0  0
  4 33  1  1  0  0  0
  2 34  1  1  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
  1 37  1  1  0  0  0
 37 38  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0064060

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@@H]2OC(=O)[C@@]3(O[C@@H]4C[C@H]5[C@@H](C[C@H](C)[C@@]4(O)C=C3C(C)=O)OC(=O)C5=C)[C@@H]2C[C@H]2O[C@@]12\C=C\C(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C29H34O9/c1-13-8-21-18(16(4)25(32)35-21)10-23-27(13,34)12-20(17(5)31)29(38-23)19-11-24-28(37-24,7-6-15(3)30)14(2)9-22(19)36-26(29)33/h6-7,12-14,18-19,21-24,34H,4,8-11H2,1-3,5H3/b7-6+/t13-,14+,18+,19+,21+,22-,23+,24+,27-,28-,29+/m0/s1

> <INCHI_KEY>
SWQFFFCGVOKUSC-HTWMNQKCSA-N

> <FORMULA>
C29H34O9

> <MOLECULAR_WEIGHT>
526.582

> <EXACT_MASS>
526.220282675

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
54.79723215026992

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,1'R,3R,3'R,5R,6R,7'R,8S,9'S,10'R,11R)-12'-acetyl-10'-hydroxy-6,9'-dimethyl-4'-methylidene-5-[(1E)-3-oxobut-1-en-1-yl]-4,6',9,14'-tetraoxaspiro[tricyclo[6.3.0.0^{3,5}]undecane-11,13'-tricyclo[8.4.0.0^{3,7}]tetradecan]-11'-ene-5',10-dione

> <ALOGPS_LOGP>
2.03

> <JCHEM_LOGP>
2.274185480333332

> <ALOGPS_LOGS>
-4.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.120954657973122

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.176460833791467

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5964157415022306

> <JCHEM_POLAR_SURFACE_AREA>
128.73000000000002

> <JCHEM_REFRACTIVITY>
133.67409999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.74e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,1'R,3R,3'R,5R,6R,7'R,8S,9'S,10'R,11R)-12'-acetyl-10'-hydroxy-6,9'-dimethyl-4'-methylidene-5-[(1E)-3-oxobut-1-en-1-yl]-4,6',9,14'-tetraoxaspiro[tricyclo[6.3.0.0^{3,5}]undecane-11,13'-tricyclo[8.4.0.0^{3,7}]tetradecan]-11'-ene-5',10-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       6.446  -1.498   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.162  -0.134   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.542   1.276   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.054   1.670   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.817   0.753   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.764  -0.786   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.933  -1.788   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.404  -1.509   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.098  -0.694   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.151   0.846   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.511   1.569   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.226   1.950   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.025   1.348   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.200   3.566   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.286  -0.019   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.012   1.290   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.356  -1.127   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -0.633  -2.486   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.884  -2.219   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.038  -3.237   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.962  -4.776   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.712  -5.675   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.771  -5.258   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.369  -3.839   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.170  -6.105   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.115  -6.308   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       0.394  -7.308   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.035  -8.772   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.121 -10.012   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -1.409  -9.842   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.739 -11.423   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.831   2.499   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.391   3.311   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       8.680  -0.394   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       8.902  -1.918   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      10.352  -2.680   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       7.521  -2.600   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       7.358  -4.185   0.000  0.00  0.00           C+0
CONECT    1    2    7   37                                                  
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   33                                                  
CONECT    5    4    6   11   32                                             
CONECT    6    5    7    8                                                  
CONECT    7    6    1                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10   15   19                                             
CONECT   10    9   11   12                                                  
CONECT   11   10    5                                                       
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    9   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   24                                                  
CONECT   19   18    9   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   26                                                  
CONECT   22   21   23   26   27                                             
CONECT   23   22   24   25                                                  
CONECT   24   23   18                                                       
CONECT   25   23                                                            
CONECT   26   22   21                                                       
CONECT   27   22   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32    5                                                            
CONECT   33    4                                                            
CONECT   34    2   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35    1   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₄O₉

Average Mass

526.5820 Da

Monoisotopic Mass

526.22028 Da

IUPAC Name

(1R,1'R,3R,3'R,5R,6R,7'R,8S,9'S,10'R,11R)-12'-acetyl-10'-hydroxy-6,9'-dimethyl-4'-methylidene-5-[(1E)-3-oxobut-1-en-1-yl]-4,6',9,14'-tetraoxaspiro[tricyclo[6.3.0.0^{3,5}]undecane-11,13'-tricyclo[8.4.0.0^{3,7}]tetradecan]-11'-ene-5',10-dione

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@@H]2OC(=O)[C@@]3(O[C@@H]4C[C@H]5[C@@H](C[C@H](C)[C@@]4(O)C=C3C(C)=O)OC(=O)C5=C)[C@@H]2C[C@H]2O[C@@]12\C=C\C(C)=O

InChI Identifier

InChI=1S/C29H34O9/c1-13-8-21-18(16(4)25(32)35-21)10-23-27(13,34)12-20(17(5)31)29(38-23)19-11-24-28(37-24,7-6-15(3)30)14(2)9-22(19)36-26(29)33/h6-7,12-14,18-19,21-24,34H,4,8-11H2,1-3,5H3/b7-6+/t13-,14+,18+,19+,21+,22-,23+,24+,27-,28-,29+/m0/s1

InChI Key

SWQFFFCGVOKUSC-HTWMNQKCSA-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
Xanthium pungens	Plant	KNApSAcK
Xanthium strumarium	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthanolides. These are sesquiterpenoids with a structure based on the xanthanolide skeleton consistsing of a cycloheptane ring usually attached to a four-carbon chain (at carbon 1 ) and a methyl group (at carbon 10), and fused to a five-member lactone ring (sharing carbons 7 and 8). The lactone ring can be conjugated with a methyl or methylene group at position 11.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Xanthanolides

Alternative Parents

Substituents

Xanthanolide-skeleton
Sesquiterpenoid
Dicarboxylic acid or derivatives
Gamma butyrolactone
Pyran
Acryloyl-group
Cyclic alcohol
Enone
Alpha,beta-unsaturated ketone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Tertiary alcohol
Carboxylic acid ester
Ketone
Lactone
Organoheterocyclic compound
Ether
Oxirane
Oxacycle
Dialkyl ether
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Alcohol
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	2.03	ALOGPS
logP	2.27	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	13.18	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	128.73 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	133.67 m³·mol⁻¹	ChemAxon
Polarizability	54.8 Å³	ChemAxon
Number of Rings	6	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

30815225

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73348840

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Pungiolide B (NP0064060)

MOL for NP0064060 (Pungiolide B)

3D MOL for NP0064060 (Pungiolide B)

3D SDF for NP0064060 (Pungiolide B)

3D-SDF for NP0064060 (Pungiolide B)

PDB for NP0064060 (Pungiolide B)

3D PDB for NP0064060 (Pungiolide B)

SMILES for NP0064060 (Pungiolide B)

INCHI for NP0064060 (Pungiolide B)

Structure for NP0064060 (Pungiolide B)

3D Structure for NP0064060 (Pungiolide B)