NP-MRD: Showing NP-Card for Cytochalasin II (NP0075257)

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Record Information

Version

2.0

Created at

2022-04-28 20:33:55 UTC

Updated at

2022-04-28 20:33:55 UTC

NP-MRD ID

NP0075257

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytochalasin II

Description

(3S,4S,6S,6aR,10S,12R,15aS,15bR)-3-benzyl-1,6,12-trihydroxy-4,10,12-trimethyl-5-methylidene-3H,4H,5H,6H,6aH,9H,10H,11H,12H,13H,14H,15H,15bH-cycloundeca[e]isoindol-15-one belongs to the class of organic compounds known as cytochalasans. These are fungal metabolites structurally characterized by the presence of an isoindolone nucleus fused to a macrocyclic ring, which can either a lactone, as in cytochalasin B, a carbonate, as in cytochalasin E, or a carbocycle, as in cytochalasin D, H, and K. Cytochalasin II is found in Daldinia concenitrica, Daldinia eschscholtzii and Daldinia eschscholzii. Based on a literature review very few articles have been published on (3S,4S,6S,6aR,10S,12R,15aS,15bR)-3-benzyl-1,6,12-trihydroxy-4,10,12-trimethyl-5-methylidene-3H,4H,5H,6H,6aH,9H,10H,11H,12H,13H,14H,15H,15bH-cycloundeca[e]isoindol-15-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282222332D          

 33 36  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282222332D          

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M  END
> <DATABASE_ID>
NP0075257

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](CC3=CC=CC=C3)NC(=O)[C@@]22[C@@H](\C=C\C[C@H](C)C[C@](C)(O)CCC2=O)[C@H](O)C1=C

> <INCHI_IDENTIFIER>
InChI=1S/C28H37NO4/c1-17-9-8-12-21-25(31)19(3)18(2)24-22(15-20-10-6-5-7-11-20)29-26(32)28(21,24)23(30)13-14-27(4,33)16-17/h5-8,10-12,17-18,21-22,24-25,31,33H,3,9,13-16H2,1-2,4H3,(H,29,32)/b12-8+/t17-,18+,21-,22-,24-,25+,27+,28+/m0/s1

> <INCHI_KEY>
NJKNOVMUCDFVLS-KKOPAYBFSA-N

> <FORMULA>
C28H37NO4

> <MOLECULAR_WEIGHT>
451.607

> <EXACT_MASS>
451.272258675

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
51.27359768177307

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,6S,6aR,10S,12R,15aR,15bR)-3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-1H,2H,3H,4H,5H,6H,6aH,9H,10H,11H,12H,13H,14H,15H,15bH-cycloundeca[e]isoindole-1,15-dione

> <ALOGPS_LOGP>
3.23

> <JCHEM_LOGP>
3.5431580410000003

> <ALOGPS_LOGS>
-4.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.535476443542429

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.951302643224604

> <JCHEM_PKA_STRONGEST_BASIC>
-2.405086470674603

> <JCHEM_POLAR_SURFACE_AREA>
86.63000000000001

> <JCHEM_REFRACTIVITY>
130.1753

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.81e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S,6S,6aR,10S,12R,15aR,15bR)-3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-2H,3H,4H,6H,6aH,9H,10H,11H,13H,14H,15bH-cycloundeca[e]isoindole-1,15-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       7.904  -1.773   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.921  -1.342   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.955  -2.483   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.189  -3.819   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.473  -5.480   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.331  -6.514   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.865  -6.043   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.342  -4.150   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.876  -3.678   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.308  -5.402   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.750  -2.560   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.891  -1.526   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.357  -1.998   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.682  -3.503   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.992  -4.313   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.650  -4.750   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.184  -4.279   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.743  -4.840   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       2.596  -3.812   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       3.218  -2.404   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.444  -1.072   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       3.468  -6.355   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.018  -6.874   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.744  -8.390   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.294  -8.909   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.881  -7.914   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.606  -6.398   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.844  -5.879   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.517  -6.023   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       8.499  -0.964   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       9.324  -7.691   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       7.911  -7.996   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      10.705  -4.088   0.000  0.00  0.00           C+0
CONECT    1    2   12                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   33                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   31   32                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   17   20                                             
CONECT   12   11    1   13                                                  
CONECT   13   12   14   30                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   29                                                  
CONECT   17   16   11   18                                                  
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19   11   21                                                  
CONECT   21   20                                                            
CONECT   22   18   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   23                                                       
CONECT   29   16                                                            
CONECT   30   13                                                            
CONECT   31    6                                                            
CONECT   32    6                                                            
CONECT   33    4                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₇NO₄

Average Mass

451.6070 Da

Monoisotopic Mass

451.27226 Da

IUPAC Name

(3S,4S,6S,6aR,10S,12R,15aR,15bR)-3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-1H,2H,3H,4H,5H,6H,6aH,9H,10H,11H,12H,13H,14H,15H,15bH-cycloundeca[e]isoindole-1,15-dione

Traditional Name

(3S,4S,6S,6aR,10S,12R,15aR,15bR)-3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-2H,3H,4H,6H,6aH,9H,10H,11H,13H,14H,15bH-cycloundeca[e]isoindole-1,15-dione

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](CC3=CC=CC=C3)NC(=O)[C@@]22[C@@H](\C=C\C[C@H](C)C[C@](C)(O)CCC2=O)[C@H](O)C1=C

InChI Identifier

InChI=1S/C28H37NO4/c1-17-9-8-12-21-25(31)19(3)18(2)24-22(15-20-10-6-5-7-11-20)29-26(32)28(21,24)23(30)13-14-27(4,33)16-17/h5-8,10-12,17-18,21-22,24-25,31,33H,3,9,13-16H2,1-2,4H3,(H,29,32)/b12-8+/t17-,18+,21-,22-,24-,25+,27+,28+/m0/s1

InChI Key

NJKNOVMUCDFVLS-KKOPAYBFSA-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
Daldinia concenitrica	Fungi	KNApSAcK
Daldinia eschscholtzii	LOTUS Database	35616633
Daldinia eschscholzii	Fungi	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cytochalasans. These are fungal metabolites structurally characterized by the presence of an isoindolone nucleus fused to a macrocyclic ring, which can either a lactone, as in cytochalasin B, a carbonate, as in cytochalasin E, or a carbocycle, as in cytochalasin D, H, and K.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Cytochalasans

Sub Class

Not Available

Direct Parent

Cytochalasans

Alternative Parents

Substituents

Carbocyclic cytochalasan skeleton
Cytochalasan
Isoindolone
Isoindoline
Isoindole
Isoindole or derivatives
Monocyclic benzene moiety
Benzenoid
Pyrrolidone
2-pyrrolidone
Cyclic alcohol
Pyrrolidine
Tertiary alcohol
Secondary alcohol
Secondary carboxylic acid amide
Carboxamide group
Ketone
Lactam
Organoheterocyclic compound
Azacycle
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	3.23	ALOGPS
logP	3.54	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	13.95	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.63 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	130.18 m³·mol⁻¹	ChemAxon
Polarizability	51.27 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

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

15223847

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Cytochalasin II (NP0075257)

MOL for NP0075257 (Cytochalasin II)

3D MOL for NP0075257 (Cytochalasin II)

3D SDF for NP0075257 (Cytochalasin II)

3D-SDF for NP0075257 (Cytochalasin II)

PDB for NP0075257 (Cytochalasin II)

3D PDB for NP0075257 (Cytochalasin II)

SMILES for NP0075257 (Cytochalasin II)

INCHI for NP0075257 (Cytochalasin II)

Structure for NP0075257 (Cytochalasin II)

3D Structure for NP0075257 (Cytochalasin II)