NP-MRD: Showing NP-Card for Cytochalasin D (NP0137229)

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Record Information

Version

2.0

Created at

2022-05-30 16:45:55 UTC

Updated at

2022-05-30 16:45:55 UTC

NP-MRD ID

NP0137229

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytochalasin D

Description

3-Benzyl-1,6,12-trihydroxy-4,10,12-trimethyl-5-methylidene-11-oxo-3H,4H,5H,6H,6aH,9H,10H,11H,12H,15H,15bH-cycloundeca[e]isoindol-15-yl acetate 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 D is found in Ascochyta rabiei, Taxus mairei, Xylaria mellissii and Zygosporium masonii. 3-Benzyl-1,6,12-trihydroxy-4,10,12-trimethyl-5-methylidene-11-oxo-3H,4H,5H,6H,6aH,9H,10H,11H,12H,15H,15bH-cycloundeca[e]isoindol-15-yl acetate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171503022D          

 37 40  0  0  0  0            999 V2000
    6.5019    0.6416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7616    1.1262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6111    0.3151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7931    0.2077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4382    0.9524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200    1.3340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9653    0.8320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9804   -0.0244    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5240    0.6258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.2707    2.1982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.3389    4.6375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3454    5.6518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 16 21  1  0  0  0  0
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  6 25  1  0  0  0  0
 13 25  1  0  0  0  0
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 33 35  1  0  0  0  0
 33 36  1  0  0  0  0
  2 36  1  0  0  0  0
 36 37  2  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1533004171503022D          

 37 40  0  0  0  0            999 V2000
    6.5019    0.6416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  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
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 14 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
  6 25  1  0  0  0  0
 13 25  1  0  0  0  0
 25 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
 31 26  1  4  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 33 36  1  0  0  0  0
  2 36  1  0  0  0  0
 36 37  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0137229

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1C2C(CC3=CC=CC=C3)NC(=O)C22C(C=CCC(C)C(=O)C(C)(O)C=CC2OC(C)=O)C(O)C1=C

> <INCHI_IDENTIFIER>
InChI=1S/C30H37NO6/c1-17-10-9-13-22-26(33)19(3)18(2)25-23(16-21-11-7-6-8-12-21)31-28(35)30(22,25)24(37-20(4)32)14-15-29(5,36)27(17)34/h6-9,11-15,17-18,22-26,33,36H,3,10,16H2,1-2,4-5H3,(H,31,35)

> <INCHI_KEY>
SDZRWUKZFQQKKV-UHFFFAOYSA-N

> <FORMULA>
C30H37NO6

> <MOLECULAR_WEIGHT>
507.627

> <EXACT_MASS>
507.262087915

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
54.096357432726975

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-1,11-dioxo-1H,2H,3H,4H,5H,6H,6aH,9H,10H,11H,12H,15H,15bH-cycloundeca[e]isoindol-15-yl acetate

> <ALOGPS_LOGP>
2.89

> <JCHEM_LOGP>
3.1152402896666667

> <ALOGPS_LOGS>
-4.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.004612692893485

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.848232228884065

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3728268033187402

> <JCHEM_POLAR_SURFACE_AREA>
112.93

> <JCHEM_REFRACTIVITY>
141.5228

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.80e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cytochalasin D

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      12.137   1.198   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.755   2.102   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.474   0.588   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.947   0.388   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.285   1.778   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.757   2.490   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.535   1.553   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.563  -0.046   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.113   2.143   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.845   1.168   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.912   3.670   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.372   4.103   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.134   4.607   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.256   6.142   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.965   7.139   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.366   8.657   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.273   9.741   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.666  11.231   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.152  11.635   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.245  10.550   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.852   9.061   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       6.753   6.501   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       7.125   5.245   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.886   5.432   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.557   4.017   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.779   4.954   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.003   6.787   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       9.016   8.065   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       8.449   9.496   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      10.539   7.840   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.201   4.364   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.423   5.302   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      11.846   4.712   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.731   6.088   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      13.501   4.783   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      12.047   3.185   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      13.687   2.871   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   36                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   25                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   25                                                  
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   14   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    6   13   26                                             
CONECT   26   25   27   31                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   26   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   35   36                                             
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   33    2   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Value	Source
3-Benzyl-1,6,12-trihydroxy-4,10,12-trimethyl-5-methylidene-11-oxo-3H,4H,5H,6H,6ah,9H,10H,11H,12H,15H,15BH-cycloundeca[e]isoindol-15-yl acetic acid	Generator

Chemical Formula

C₃₀H₃₇NO₆

Average Mass

507.6270 Da

Monoisotopic Mass

507.26209 Da

IUPAC Name

3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-1,11-dioxo-1H,2H,3H,4H,5H,6H,6aH,9H,10H,11H,12H,15H,15bH-cycloundeca[e]isoindol-15-yl acetate

Traditional Name

cytochalasin D

CAS Registry Number

Not Available

SMILES

CC1C2C(CC3=CC=CC=C3)NC(=O)C22C(C=CCC(C)C(=O)C(C)(O)C=CC2OC(C)=O)C(O)C1=C

InChI Identifier

InChI=1S/C30H37NO6/c1-17-10-9-13-22-26(33)19(3)18(2)25-23(16-21-11-7-6-8-12-21)31-28(35)30(22,25)24(37-20(4)32)14-15-29(5,36)27(17)34/h6-9,11-15,17-18,22-26,33,36H,3,10,16H2,1-2,4-5H3,(H,31,35)

InChI Key

SDZRWUKZFQQKKV-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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 rabiei	LOTUS Database	35616633
Taxus mairei	LOTUS Database	35616633
Xylaria mellissii	LOTUS Database	35616633
Zygosporium masonii	LOTUS Database	35616633

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
Acyloin
Monocyclic benzene moiety
Benzenoid
Pyrrolidone
2-pyrrolidone
Cyclic alcohol
Pyrrolidine
Tertiary alcohol
Secondary alcohol
Secondary carboxylic acid amide
Carboxamide group
Carboxylic acid ester
Cyclic ketone
Ketone
Lactam
Organoheterocyclic compound
Azacycle
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Organic oxygen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Alcohol
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	2.89	ALOGPS
logP	3.12	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	12.85	ChemAxon
pKa (Strongest Basic)	-0.37	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	112.93 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	141.52 m³·mol⁻¹	ChemAxon
Polarizability	54.1 Å³	ChemAxon
Number of Rings	4	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

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

30956

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cytochalasin D (NP0137229)

MOL for NP0137229 (Cytochalasin D)

3D MOL for NP0137229 (Cytochalasin D)

3D SDF for NP0137229 (Cytochalasin D)

3D-SDF for NP0137229 (Cytochalasin D)

PDB for NP0137229 (Cytochalasin D)

3D PDB for NP0137229 (Cytochalasin D)

SMILES for NP0137229 (Cytochalasin D)

INCHI for NP0137229 (Cytochalasin D)

Structure for NP0137229 (Cytochalasin D)

3D Structure for NP0137229 (Cytochalasin D)