NP-MRD: Showing NP-Card for (3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol (NP0219294)

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Record Information

Version

2.0

Created at

2022-09-05 20:14:20 UTC

Updated at

2022-09-05 20:14:21 UTC

NP-MRD ID

NP0219294

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol

Description

Cytochalasin S 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. Based on a literature review very few articles have been published on Cytochalasin S.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052222142D          

 34 37  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052222142D          

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 30 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  6  0  0  0
 31 34  1  0  0  0  0
  2 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0219294

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@@H](O)[C@@H]2\C=C/C[C@H](C)C[C@@](C)(O)\C=C/[C@@H](O)[C@@]22[C@H]([C@H](CC3=CC=CC=C3)N=C2O)[C@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C28H39NO5/c1-17-9-8-12-20-23(31)18(2)27(4,34)24-21(15-19-10-6-5-7-11-19)29-25(32)28(20,24)22(30)13-14-26(3,33)16-17/h5-8,10-14,17-18,20-24,30-31,33-34H,9,15-16H2,1-4H3,(H,29,32)/b12-8-,14-13-/t17-,18-,20-,21-,22+,23+,24+,26-,27+,28+/m0/s1

> <INCHI_KEY>
IWNYMETYLRNJJP-JLHBQRKXSA-N

> <FORMULA>
C28H39NO5

> <MOLECULAR_WEIGHT>
469.622

> <EXACT_MASS>
469.28282336

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
52.04857437220134

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,5S,6S,6aR,10S,12R,15R,15aS,15bR)-3-benzyl-4,5,10,12-tetramethyl-3H,4H,5H,6H,6aH,9H,10H,11H,12H,15H,15bH-cycloundeca[e]isoindole-1,4,6,12,15-pentol

> <JCHEM_LOGP>
1.860897507956452

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.863171460766633

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.280220570132168

> <JCHEM_PKA_STRONGEST_BASIC>
5.641362143834114

> <JCHEM_POLAR_SURFACE_AREA>
113.51

> <JCHEM_REFRACTIVITY>
134.1889

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S,5S,6S,6aR,10S,12R,15R,15aS,15bR)-3-benzyl-4,5,10,12-tetramethyl-3H,5H,6H,6aH,9H,10H,11H,15H,15bH-cycloundeca[e]isoindole-1,4,6,12,15-pentol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      10.736   2.376   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.441   3.208   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.277   2.200   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.752   1.981   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.352   2.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.519   3.916   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.185   3.146   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.185   1.606   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.852   3.916   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.518   3.146   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.852   5.456   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.335   5.188   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.325   6.903   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.185   6.226   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.506   7.732   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.475   8.877   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.951  10.341   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.921  11.486   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.396  12.950   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.903  13.270   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.933  12.126   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.457  10.661   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       5.037   7.893   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       5.838   6.356   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       7.170   6.166   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.519   5.456   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.352   6.751   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.343   7.915   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.752   7.391   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.277   7.172   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.441   6.163   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.013   7.593   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.979   6.090   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       9.875   4.686   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   26                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11   15   26                                                  
CONECT   15   14   16   23                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   17                                                       
CONECT   23   15   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24    6   14   27                                             
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33   34                                             
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34   31    2                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₉NO₅

Average Mass

469.6220 Da

Monoisotopic Mass

469.28282 Da

IUPAC Name

(3S,4S,5S,6S,6aR,10S,12R,15R,15aS,15bR)-3-benzyl-4,5,10,12-tetramethyl-3H,4H,5H,6H,6aH,9H,10H,11H,12H,15H,15bH-cycloundeca[e]isoindole-1,4,6,12,15-pentol

Traditional Name

(3S,4S,5S,6S,6aR,10S,12R,15R,15aS,15bR)-3-benzyl-4,5,10,12-tetramethyl-3H,5H,6H,6aH,9H,10H,11H,15H,15bH-cycloundeca[e]isoindole-1,4,6,12,15-pentol

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@@H](O)[C@@H]2\C=C/C[C@H](C)C[C@@](C)(O)\C=C/[C@@H](O)[C@@]22[C@H]([C@H](CC3=CC=CC=C3)N=C2O)[C@]1(C)O

InChI Identifier

InChI=1S/C28H39NO5/c1-17-9-8-12-20-23(31)18(2)27(4,34)24-21(15-19-10-6-5-7-11-19)29-25(32)28(20,24)22(30)13-14-26(3,33)16-17/h5-8,10-14,17-18,20-24,30-31,33-34H,9,15-16H2,1-4H3,(H,29,32)/b12-8-,14-13-/t17-,18-,20-,21-,22+,23+,24+,26-,27+,28+/m0/s1

InChI Key

IWNYMETYLRNJJP-JLHBQRKXSA-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

Not Available

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

Cytochalasan
Carbocyclic cytochalasan skeleton
Isoindolone
Isoindole or derivatives
Isoindole
Isoindoline
Benzenoid
2-pyrrolidone
Pyrrolidone
Monocyclic benzene moiety
Tertiary alcohol
Pyrrolidine
Cyclic alcohol
Secondary carboxylic acid amide
Secondary alcohol
Lactam
Carboxamide group
Azacycle
Organoheterocyclic compound
Polyol
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
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	1.86	ChemAxon
pKa (Strongest Acidic)	3.28	ChemAxon
pKa (Strongest Basic)	5.64	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	113.51 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	134.19 m³·mol⁻¹	ChemAxon
Polarizability	52.05 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

C00011350

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

101588730

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol (NP0219294)

MOL for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

3D MOL for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

3D SDF for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

3D-SDF for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

PDB for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

3D PDB for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

SMILES for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

INCHI for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

Structure for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)

3D Structure for NP0219294 ((3s,3ar,4s,5s,6s,6ar,10s,12r,15r,15as)-3-benzyl-4,5,10,12-tetramethyl-3h,3ah,5h,6h,6ah,9h,10h,11h,15h-cycloundeca[d]isoindole-1,4,6,12,15-pentol)