NP-MRD: Showing NP-Card for Cytochalasin B (NP0058024)

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Record Information

Version

2.0

Created at

2022-04-28 03:21:31 UTC

Updated at

2022-04-28 03:21:31 UTC

NP-MRD ID

NP0058024

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytochalasin B

Description

Cytochalasin B, also known as phomin, belongs to the class of organic compounds known as cytochalasins. These are cytochalasans in which the hydrogenated isoindolone bears a benzyl group. Thus, cytochalasin b is considered to be a cytochalasin. Cytochalasin B is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Cytochalasin B is found in Ascochyta heteromorpha, Phoma exigua var. exigua, Cirsium arvense, Cochliobolus lunatus, Drechslera biseptata, Gnomonia erythrostoma, Helminthosporium dematioideum, Hormiscium spp., Hypomyces odoratus, Boeremia exigua, Pyrenophora semeniperda and Sonchus mauritanicus. Cytochalasin B was first documented in 2022 (PMID: 35455997). Based on a literature review a small amount of articles have been published on cytochalasin B (PMID: 35382968) (PMID: 35335252) (PMID: 35305656) (PMID: 35268792).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652304282205212D          

 35 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END

  Mrv1652304282205212D          

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 24 25  2  0  0  0  0
 26 25  1  1  0  0  0
 12 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31  8  1  1  0  0  0
 12 31  1  0  0  0  0
 30 32  1  1  0  0  0
 27 33  1  6  0  0  0
 22 34  1  1  0  0  0
 18 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0058024

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](CC3=CC=CC=C3)NC(=O)[C@]22OC(=O)\C=C\[C@H](O)CCC[C@@H](C)C\C=C\[C@H]2[C@H](O)C1=C

> <INCHI_IDENTIFIER>
InChI=1S/C29H37NO5/c1-18-9-7-13-22(31)15-16-25(32)35-29-23(14-8-10-18)27(33)20(3)19(2)26(29)24(30-28(29)34)17-21-11-5-4-6-12-21/h4-6,8,11-12,14-16,18-19,22-24,26-27,31,33H,3,7,9-10,13,17H2,1-2H3,(H,30,34)/b14-8+,16-15+/t18-,19-,22-,23+,24+,26+,27-,29-/m1/s1

> <INCHI_KEY>
GBOGMAARMMDZGR-TYHYBEHESA-N

> <FORMULA>
C29H37NO5

> <MOLECULAR_WEIGHT>
479.617

> <EXACT_MASS>
479.267173295

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
51.95219386339603

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5R,9R,13S,15S,15aS,16S,18aS,18bS)-16-benzyl-5,13-dihydroxy-9,15-dimethyl-14-methylidene-2H,5H,6H,7H,8H,9H,10H,13H,14H,15H,15aH,16H,17H,18H,18bH-oxacyclotetradeca[3,2-e]isoindole-2,18-dione

> <ALOGPS_LOGP>
4.05

> <JCHEM_LOGP>
4.082356843333333

> <ALOGPS_LOGS>
-4.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.162264371801953

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.110296765877077

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8716115820565564

> <JCHEM_POLAR_SURFACE_AREA>
95.86

> <JCHEM_REFRACTIVITY>
136.417

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.14e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cytochalasin B

> <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      10.152   2.953   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.338   1.645   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.799   1.696   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.074   3.055   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.888   4.362   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.427   4.311   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.986   0.389   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.711  -0.970   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       9.236  -1.181   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       9.502  -2.480   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.892  -3.370   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       8.148  -3.423   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.628  -2.996   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       9.997  -1.501   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.888  -0.433   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.477  -1.074   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.587  -2.142   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.066  -1.714   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      15.176  -2.782   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      14.806  -4.277   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.327  -4.704   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.957  -6.199   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.477  -6.626   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.367  -5.558   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.888  -5.986   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.778  -4.918   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.298  -5.345   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.189  -4.277   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.709  -4.704   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.559  -2.782   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.038  -2.355   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.449  -1.714   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.929  -6.840   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      14.066  -7.267   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      14.436  -0.219   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    3    8                                                       
CONECT    8    7    9   31                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   26   31                                             
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   35                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   34                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   12   27                                                  
CONECT   27   26   28   33                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30    8   12                                                  
CONECT   32   30                                                            
CONECT   33   27                                                            
CONECT   34   22                                                            
CONECT   35   18                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
Phomin	ChEBI

Chemical Formula

C₂₉H₃₇NO₅

Average Mass

479.6170 Da

Monoisotopic Mass

479.26717 Da

IUPAC Name

(5R,9R,13S,15S,15aS,16S,18aS,18bS)-16-benzyl-5,13-dihydroxy-9,15-dimethyl-14-methylidene-2H,5H,6H,7H,8H,9H,10H,13H,14H,15H,15aH,16H,17H,18H,18bH-oxacyclotetradeca[3,2-e]isoindole-2,18-dione

Traditional Name

cytochalasin B

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](CC3=CC=CC=C3)NC(=O)[C@]22OC(=O)\C=C\[C@H](O)CCC[C@@H](C)C\C=C\[C@H]2[C@H](O)C1=C

InChI Identifier

InChI=1S/C29H37NO5/c1-18-9-7-13-22(31)15-16-25(32)35-29-23(14-8-10-18)27(33)20(3)19(2)26(29)24(30-28(29)34)17-21-11-5-4-6-12-21/h4-6,8,11-12,14-16,18-19,22-24,26-27,31,33H,3,7,9-10,13,17H2,1-2H3,(H,30,34)/b14-8+,16-15+/t18-,19-,22-,23+,24+,26+,27-,29-/m1/s1

InChI Key

GBOGMAARMMDZGR-TYHYBEHESA-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
Ascochyta heteromorpha	Fungi	KNApSAcK
Boeremia exigua var. exigua	Fungi	KNApSAcK
Cirsium arvense	LOTUS Database	35616633
Curvularia lunata	Fungi	KNApSAcK
Drechslera biseptata	Fungi	KNApSAcK
Gnomonia erythrostoma	Fungi	KNApSAcK
Helminthosporium dematioideum	Fungi	KNApSAcK
Hormiscium spp.	-	KNApSAcK
Hypomyces odoratus	Fungi	KNApSAcK
Phoma exigua	LOTUS Database	35616633
Pyrenophora seminiperda	Fungi	KNApSAcK
Sonchus mauritanicus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cytochalasins. These are cytochalasans in which the hydrogenated isoindolone bears a benzyl group.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Cytochalasans

Sub Class

Cytochalasins

Direct Parent

Cytochalasins

Alternative Parents

Substituents

Lactone cytochalasin skeleton
Cytochalasin
Isoindolone
Isoindoline
Isoindole
Isoindole or derivatives
Monocyclic benzene moiety
Pyrrolidone
Benzenoid
2-pyrrolidone
Cyclic alcohol
Pyrrolidine
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Carboxylic acid ester
Lactam
Lactone
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Organopnictogen compound
Organic oxygen compound
Alcohol
Organonitrogen compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic heterotricyclic compound (CHEBI:23527 )
lactam (CHEBI:23527 )
lactone (CHEBI:23527 )
cytochalasin (CHEBI:23527 )
Cytochalasins (LMPK11000002 )

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	4.05	ALOGPS
logP	4.08	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	13.11	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	95.86 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	136.42 m³·mol⁻¹	ChemAxon
Polarizability	51.95 Å³	ChemAxon
Number of Rings	4	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

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Cytochalasin_B

METLIN ID

Not Available

PubChem Compound

5311281

PDB ID

Not Available

ChEBI ID

23527

Good Scents ID

rw1233461

References

General References

Bianchi F, Sommariva M, Cornaghi LB, Denti L, Nava A, Arnaboldi F, Moscheni C, Gagliano N: Mechanical Cues, E-Cadherin Expression and Cell "Sociality" Are Crucial Crossroads in Determining Pancreatic Ductal Adenocarcinoma Cells Behavior. Cells. 2022 Apr 13;11(8). pii: cells11081318. doi: 10.3390/cells11081318. [PubMed:35455997 ]
Kanamori T, Miki Y, Katou M, Ogura SI, Yuasa H: 4'-Nitrobiphenyl thioglucoside as the Smallest, fluorescent photosensitizer with cancer targeting ligand. Bioorg Med Chem. 2022 May 1;61:116737. doi: 10.1016/j.bmc.2022.116737. Epub 2022 Mar 29. [PubMed:35382968 ]
Lan YH, Chen IH, Lu HH, Guo TJ, Hwang TL, Leu YL: Euphormins A and B, New Pyranocoumarin Derivatives from Euphorbia formosana Hayata, and Their Anti-Inflammatory Activity. Molecules. 2022 Mar 14;27(6). pii: molecules27061885. doi: 10.3390/molecules27061885. [PubMed:35335252 ]
Li Y, Tu Q, Xie D, Chen S, Gao K, Xu X, Zhang Z, Mei X: Triamcinolone acetonide-loaded nanoparticles encapsulated by CD90(+) MCSs-derived microvesicles drive anti-inflammatory properties and promote cartilage regeneration after osteoarthritis. J Nanobiotechnology. 2022 Mar 19;20(1):150. doi: 10.1186/s12951-022-01367-z. [PubMed:35305656 ]
Magiera A, Czerwinska ME, Owczarek A, Marchelak A, Granica S, Olszewska MA: Polyphenol-Enriched Extracts of Prunus spinosa Fruits: Anti-Inflammatory and Antioxidant Effects in Human Immune Cells Ex Vivo in Relation to Phytochemical Profile. Molecules. 2022 Mar 4;27(5). pii: molecules27051691. doi: 10.3390/molecules27051691. [PubMed:35268792 ]

Showing NP-Card for Cytochalasin B (NP0058024)

MOL for NP0058024 (Cytochalasin B)

3D MOL for NP0058024 (Cytochalasin B)

3D SDF for NP0058024 (Cytochalasin B)

3D-SDF for NP0058024 (Cytochalasin B)

PDB for NP0058024 (Cytochalasin B)

3D PDB for NP0058024 (Cytochalasin B)

SMILES for NP0058024 (Cytochalasin B)

INCHI for NP0058024 (Cytochalasin B)

Structure for NP0058024 (Cytochalasin B)

3D Structure for NP0058024 (Cytochalasin B)