NP-MRD: Showing NP-Card for Cytochalasin R (NP0058052)

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Record Information

Version

2.0

Created at

2022-04-28 03:23:24 UTC

Updated at

2022-04-28 03:23:24 UTC

NP-MRD ID

NP0058052

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytochalasin R

Description

(1R,2R,5R,7R,9R,11R,12S,13S,15R,16R,17R,18R)-18-benzyl-5,20-dihydroxy-5,7,15,16-tetramethyl-6-oxo-10,14-dioxa-19-azapentacyclo[10.8.0.0¹,¹⁷.0⁹,¹¹.0¹³,¹⁵]Icosa-3,19-dien-2-yl acetate belongs to the class of organic compounds known as isoindoles and derivatives. These are polycyclic compounds containing an isoindole moiety, which is structurally characterized by a cyclohexadiene fused to a pyrrole ring. Cytochalasin R is found in Hypoxylon terricola and Phomopsis sp.. Based on a literature review very few articles have been published on (1R,2R,5R,7R,9R,11R,12S,13S,15R,16R,17R,18R)-18-benzyl-5,20-dihydroxy-5,7,15,16-tetramethyl-6-oxo-10,14-dioxa-19-azapentacyclo[10.8.0.0¹,¹⁷.0⁹,¹¹.0¹³,¹⁵]Icosa-3,19-dien-2-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282205232D          

 38 43  0  0  1  0            999 V2000
   -0.7716   -2.3761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0066   -1.3140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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 14 38  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282205232D          

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    3.0488   -5.3954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6957   -3.0415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6086   -1.4930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6485   -2.7421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9320   -3.7073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4882   -3.6868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  3  7  1  0  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 12 10  1  6  0  0  0
 13 12  1  1  0  0  0
  8 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
 17 16  1  6  0  0  0
 12 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 12 27  1  0  0  0  0
 27 28  1  1  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 24 32  1  6  0  0  0
 24 33  1  1  0  0  0
 21 34  1  6  0  0  0
 19 35  1  6  0  0  0
 18 35  1  6  0  0  0
 16 36  1  6  0  0  0
 15 36  1  0  0  0  0
 15 37  1  1  0  0  0
 14 38  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0058052

> <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@H]3O[C@@H]3C[C@@H](C)C(=O)[C@](C)(O)\C=C\[C@H]2OC(C)=O)[C@@H]2O[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C30H37NO7/c1-15-13-20-24(37-20)23-26-29(5,38-26)16(2)22-19(14-18-9-7-6-8-10-18)31-27(34)30(22,23)21(36-17(3)32)11-12-28(4,35)25(15)33/h6-12,15-16,19-24,26,35H,13-14H2,1-5H3,(H,31,34)/b12-11+/t15-,16-,19-,20-,21-,22+,23+,24+,26+,28-,29-,30-/m1/s1

> <INCHI_KEY>
KHJAUVJHBOZECO-HKXQFQTHSA-N

> <FORMULA>
C30H37NO7

> <MOLECULAR_WEIGHT>
523.626

> <EXACT_MASS>
523.257002535

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
54.79994595999047

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,3E,5R,7R,9R,11R,12S,13S,15R,16R,17R,18R)-18-benzyl-5-hydroxy-5,7,15,16-tetramethyl-6,20-dioxo-10,14-dioxa-19-azapentacyclo[10.8.0.0^{1,17}.0^{9,11}.0^{13,15}]icos-3-en-2-yl acetate

> <ALOGPS_LOGP>
2.76

> <JCHEM_LOGP>
2.5688497299999975

> <ALOGPS_LOGS>
-4.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.175694469143334

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.858567308659001

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3110916842672692

> <JCHEM_POLAR_SURFACE_AREA>
117.76

> <JCHEM_REFRACTIVITY>
138.0688

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.50e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3E,5R,7R,9R,11R,12S,13S,15R,16R,17R,18R)-18-benzyl-5-hydroxy-5,7,15,16-tetramethyl-6,20-dioxo-10,14-dioxa-19-azapentacyclo[10.8.0.0^{1,17}.0^{9,11}.0^{13,15}]icos-3-en-2-yl acetate

> <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      -1.440  -4.435   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.088  -4.623   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.689  -6.041   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.238  -7.271   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.766  -7.083   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.368  -5.665   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.073  -6.212   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.078  -4.853   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.540  -3.410   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.746  -2.453   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.673  -0.835   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.029  -3.304   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.620  -4.352   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.699  -5.451   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.192  -4.849   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.163  -4.015   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.520  -2.920   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.752  -4.070   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.289  -4.166   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.673  -5.657   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.373  -6.483   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.851  -8.086   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       9.257  -9.069   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       6.360  -8.470   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.935  -7.377   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.692  -6.126   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.614  -5.027   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       3.206  -6.077   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.430  -7.664   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       3.291  -8.942   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.894  -7.770   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       6.466 -10.270   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.691 -10.071   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.899  -5.677   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       8.603  -2.787   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       8.677  -5.119   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       7.340  -6.920   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.645  -6.882   0.000  0.00  0.00           C+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   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   17   27                                             
CONECT   13   12    8   14                                                  
CONECT   14   13   15   38                                                  
CONECT   15   14   16   36   37                                             
CONECT   16   15   17   36                                                  
CONECT   17   16   12   18                                                  
CONECT   18   17   19   35                                                  
CONECT   19   18   20   35                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   34                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   32   33                                             
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   12   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   24                                                            
CONECT   33   24                                                            
CONECT   34   21                                                            
CONECT   35   19   18                                                       
CONECT   36   16   15                                                       
CONECT   37   15                                                            
CONECT   38   14                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Value	Source
(1R,2R,5R,7R,9R,11R,12S,13S,15R,16R,17R,18R)-18-Benzyl-5,20-dihydroxy-5,7,15,16-tetramethyl-6-oxo-10,14-dioxa-19-azapentacyclo[10.8.0.0,.0,.0,]icosa-3,19-dien-2-yl acetic acid	Generator

Chemical Formula

C₃₀H₃₇NO₇

Average Mass

523.6260 Da

Monoisotopic Mass

523.25700 Da

IUPAC Name

(1R,2R,3E,5R,7R,9R,11R,12S,13S,15R,16R,17R,18R)-18-benzyl-5-hydroxy-5,7,15,16-tetramethyl-6,20-dioxo-10,14-dioxa-19-azapentacyclo[10.8.0.0^{1,17}.0^{9,11}.0^{13,15}]icos-3-en-2-yl acetate

Traditional Name

(1R,2R,3E,5R,7R,9R,11R,12S,13S,15R,16R,17R,18R)-18-benzyl-5-hydroxy-5,7,15,16-tetramethyl-6,20-dioxo-10,14-dioxa-19-azapentacyclo[10.8.0.0^{1,17}.0^{9,11}.0^{13,15}]icos-3-en-2-yl acetate

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@H]3O[C@@H]3C[C@@H](C)C(=O)[C@](C)(O)\C=C\[C@H]2OC(C)=O)[C@@H]2O[C@]12C

InChI Identifier

InChI=1S/C30H37NO7/c1-15-13-20-24(37-20)23-26-29(5,38-26)16(2)22-19(14-18-9-7-6-8-10-18)31-27(34)30(22,23)21(36-17(3)32)11-12-28(4,35)25(15)33/h6-12,15-16,19-24,26,35H,13-14H2,1-5H3,(H,31,34)/b12-11+/t15-,16-,19-,20-,21-,22+,23+,24+,26+,28-,29-,30-/m1/s1

InChI Key

KHJAUVJHBOZECO-HKXQFQTHSA-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
Hypoxylon terricola	Fungi	KNApSAcK
Phomopsis sp. Phomopsis sp.	Fungi	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoindoles and derivatives. These are polycyclic compounds containing an isoindole moiety, which is structurally characterized by a cyclohexadiene fused to a pyrrole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isoindoles and derivatives

Sub Class

Not Available

Direct Parent

Isoindoles and derivatives

Alternative Parents

Substituents

Isoindole or derivatives
Oxepane
Benzenoid
Monocyclic benzene moiety
Acyloin
Cyclic carboximidic acid
Tertiary alcohol
Pyrroline
Cyclic ketone
Ketone
Carboxylic acid ester
Oxacycle
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Ether
Oxirane
Dialkyl ether
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	2.76	ALOGPS
logP	2.57	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	12.86	ChemAxon
pKa (Strongest Basic)	-0.31	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	117.76 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	138.07 m³·mol⁻¹	ChemAxon
Polarizability	54.8 Å³	ChemAxon
Number of Rings	6	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

162891346

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cytochalasin R (NP0058052)

MOL for NP0058052 (Cytochalasin R)

3D MOL for NP0058052 (Cytochalasin R)

3D SDF for NP0058052 (Cytochalasin R)

3D-SDF for NP0058052 (Cytochalasin R)

PDB for NP0058052 (Cytochalasin R)

3D PDB for NP0058052 (Cytochalasin R)

SMILES for NP0058052 (Cytochalasin R)

INCHI for NP0058052 (Cytochalasin R)

Structure for NP0058052 (Cytochalasin R)

3D Structure for NP0058052 (Cytochalasin R)