NP-MRD: Showing NP-Card for (5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one (NP0207049)

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Record Information

Version

2.0

Created at

2022-09-05 03:30:20 UTC

Updated at

2022-09-05 03:30:20 UTC

NP-MRD ID

NP0207049

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one

Description

(5R,9S,13S,15R,15aS,16S)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-2H,5H,6H,7H,8H,9H,10H,13H,14H,15H,15aH,16H,18bH-oxacyclotetradeca[3,2-e]isoindol-2-one belongs to the class of organic compounds known as cytochalasins. These are cytochalasans in which the hydrogenated isoindolone bears a benzyl group. Based on a literature review very few articles have been published on (5R,9S,13S,15R,15aS,16S)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-2H,5H,6H,7H,8H,9H,10H,13H,14H,15H,15aH,16H,18bH-oxacyclotetradeca[3,2-e]isoindol-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052205302D          

 35 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052205302D          

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 14 15  1  1  0  0  0
 14 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
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
  5 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 27 32  1  0  0  0  0
 33 25  1  6  0  0  0
 21 33  1  0  0  0  0
 33 34  1  0  0  0  0
  2 34  1  0  0  0  0
 34 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0207049

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1[C@H]2[C@H](CC3=CC=CC=C3)N=C(O)C22OC(=O)\C=C\[C@H](O)CCC[C@H](C)C\C=C\C2[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?/m0/s1

> <INCHI_KEY>
GBOGMAARMMDZGR-WKODCPSNSA-N

> <FORMULA>
C29H37NO5

> <MOLECULAR_WEIGHT>
479.617

> <EXACT_MASS>
479.267173295

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
53.40861526417285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
3.5141444399224833

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.12712051751835

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.946290294944934

> <JCHEM_PKA_STRONGEST_BASIC>
4.845651102110083

> <JCHEM_POLAR_SURFACE_AREA>
99.35000000000001

> <JCHEM_REFRACTIVITY>
136.9387

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5R,9S,13S,15R,15aS,16S)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5H,6H,7H,8H,9H,10H,13H,15H,15aH,16H,18bH-oxacyclotetradeca[3,2-e]isoindol-2-one

> <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       5.045  -0.678   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.524  -1.109   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.636  -0.044   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.271   1.452   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.115  -0.475   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.227   0.589   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.706   0.158   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.818   1.223   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.297   0.792   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.409   1.856   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.663  -0.704   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      16.141  -1.135   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.507  -2.631   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.394  -3.696   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      15.760  -5.192   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      13.916  -3.265   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.803  -4.330   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.325  -3.898   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      10.212  -4.963   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      11.072  -2.216   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.480  -1.971   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.837  -2.700   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      12.224  -2.032   0.000  0.00  0.00           O+0
HETATM   24  N   UNK     0      10.563  -4.216   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       9.037  -4.423   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.307  -5.780   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.118  -7.089   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.657  -7.043   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.467  -8.352   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.738  -9.709   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.199  -9.755   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.388  -8.446   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.368  -3.036   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.889  -2.605   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.777  -3.669   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20    5   22   33                                             
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   33                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   27                                                       
CONECT   33   25   21   34                                                  
CONECT   34   33    2   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₇NO₅

Average Mass

479.6170 Da

Monoisotopic Mass

479.26717 Da

IUPAC Name

(5R,9S,13S,15R,15aS,16S)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-2H,5H,6H,7H,8H,9H,10H,13H,14H,15H,15aH,16H,18bH-oxacyclotetradeca[3,2-e]isoindol-2-one

Traditional Name

(5R,9S,13S,15R,15aS,16S)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5H,6H,7H,8H,9H,10H,13H,15H,15aH,16H,18bH-oxacyclotetradeca[3,2-e]isoindol-2-one

CAS Registry Number

Not Available

SMILES

C[C@@H]1[C@H]2[C@H](CC3=CC=CC=C3)N=C(O)C22OC(=O)\C=C\[C@H](O)CCC[C@H](C)C\C=C\C2[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?/m0/s1

InChI Key

GBOGMAARMMDZGR-WKODCPSNSA-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 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
Isoindole or derivatives
Isoindole
Isoindoline
Benzenoid
2-pyrrolidone
Pyrrolidone
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Pyrrolidine
Cyclic alcohol
Secondary carboxylic acid amide
Secondary alcohol
Lactone
Lactam
Carboxylic acid ester
Carboxamide group
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
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	3.51	ChemAxon
pKa (Strongest Acidic)	1.95	ChemAxon
pKa (Strongest Basic)	4.85	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.35 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	136.94 m³·mol⁻¹	ChemAxon
Polarizability	53.41 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

162933328

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one (NP0207049)

MOL for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

3D MOL for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

3D SDF for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

3D-SDF for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

PDB for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

3D PDB for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

SMILES for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

INCHI for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

Structure for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)

3D Structure for NP0207049 ((5r,9s,13s,15r,15as,16s)-16-benzyl-5,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[3,2-d]isoindol-2-one)