NP-MRD: Showing NP-Card for (9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one (NP0186026)

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Record Information

Version

2.0

Created at

2022-09-04 01:41:49 UTC

Updated at

2022-09-04 01:41:49 UTC

NP-MRD ID

NP0186026

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Cytochalasin Z3 belongs to the class of organic compounds known as cytochalasins. These are cytochalasans in which the hydrogenated isoindolone bears a benzyl group. (9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one is found in Pyrenophora seminiperda. (9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one was first documented in 2022 (PMID: 35100652). Based on a literature review very few articles have been published on Cytochalasin Z3.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042203412D          

 35 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309042203412D          

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 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
  6 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 17 15  1  1  0  0  0
  5 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 33 32  1  1  0  0  0
 17 33  1  0  0  0  0
 33 34  1  0  0  0  0
  2 34  1  0  0  0  0
 34 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0186026

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C29H37NO5/c1-18-9-7-13-23-27(33)20(3)19(2)26-24(17-21-10-5-4-6-11-21)30-28(34)29(23,26)35-25(32)14-8-12-22(31)16-15-18/h4-8,10-11,13-14,18-19,22-24,26-27,31,33H,3,9,12,15-17H2,1-2H3,(H,30,34)/b13-7+,14-8+/t18-,19+,22?,23-,24-,26-,27+,29+/m0/s1

> <INCHI_KEY>
CKKNSYUDGHWTMW-FGZYXACLSA-N

> <FORMULA>
C29H37NO5

> <MOLECULAR_WEIGHT>
479.617

> <EXACT_MASS>
479.267173295

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
53.11756302362475

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(9R,13S,15S,15aS,16S,18aS,18bS)-16-benzyl-6,13,18-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>
3.358230079097893

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.221913147637409

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9465396861141233

> <JCHEM_PKA_STRONGEST_BASIC>
4.845651442149344

> <JCHEM_POLAR_SURFACE_AREA>
99.35000000000001

> <JCHEM_REFRACTIVITY>
137.0927

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(9R,13S,15S,15aS,16S,18aS,18bS)-16-benzyl-6,13,18-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                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       3.709  -4.704   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.189  -4.277   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.559  -2.782   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.449  -1.714   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.038  -2.355   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.711  -0.970   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.986   0.389   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.799   1.696   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.074   3.055   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.888   4.362   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.427   4.311   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.152   2.953   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.338   1.645   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       9.236  -1.181   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       9.502  -2.480   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      10.892  -3.370   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.148  -3.423   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.628  -2.996   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.997  -1.501   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.888  -0.433   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      11.477  -1.074   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.587  -2.142   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      14.066  -1.714   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      15.176  -2.782   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      16.656  -2.355   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      14.806  -4.277   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.327  -4.704   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.957  -6.199   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      14.066  -7.267   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.477  -6.626   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.367  -5.558   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.888  -5.986   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.778  -4.918   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.298  -5.345   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       5.929  -6.840   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   17                                                  
CONECT    6    5    7   14                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14    6   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    5   18   33                                             
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   17   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

(9R,13S,15S,15aS,16S,18aS,18bS)-16-benzyl-6,13,18-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

(9R,13S,15S,15aS,16S,18aS,18bS)-16-benzyl-6,13,18-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)[C@]22OC(=O)\C=C\CC(O)CC[C@@H](C)C\C=C\[C@H]2[C@H](O)C1=C

InChI Identifier

InChI=1S/C29H37NO5/c1-18-9-7-13-23-27(33)20(3)19(2)26-24(17-21-10-5-4-6-11-21)30-28(34)29(23,26)35-25(32)14-8-12-22(31)16-15-18/h4-8,10-11,13-14,18-19,22-24,26-27,31,33H,3,9,12,15-17H2,1-2H3,(H,30,34)/b13-7+,14-8+/t18-,19+,22?,23-,24-,26-,27+,29+/m0/s1

InChI Key

CKKNSYUDGHWTMW-FGZYXACLSA-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
Pyrenophora seminiperda	LOTUS Database	35616633

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
Isoindoline
Isoindole
Isoindole or derivatives
Monocyclic benzene moiety
Pyrrolidone
Benzenoid
2-pyrrolidone
Cyclic alcohol
Pyrrolidine
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Carboxylic acid ester
Lactam
Lactone
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Organopnictogen compound
Organic oxygen compound
Alcohol
Organonitrogen compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organic nitrogen 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	3.36	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	137.09 m³·mol⁻¹	ChemAxon
Polarizability	53.12 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

C00044679

Chemspider ID

31148405

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

76322840

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Peng X, Ouyang Q, Pei J, Chang J, Qin C, Ruan H: TRAIL-sensitizing Cytochalasins from the Endophytic Fungus Phoma multirostrata. Planta Med. 2022 Nov;88(14):1299-1310. doi: 10.1055/a-1755-5411. Epub 2022 Jan 31. [PubMed:35100652 ]
LOTUS database [Link]

Showing NP-Card for (9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one (NP0186026)

MOL for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

3D MOL for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

3D SDF for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

3D-SDF for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

PDB for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

3D PDB for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

SMILES for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

INCHI for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

Structure for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)

3D Structure for NP0186026 ((9r,12as,13s,15s,15as,16s,18as)-16-benzyl-6,13,18-trihydroxy-9,15-dimethyl-14-methylidene-5h,6h,7h,8h,9h,10h,12ah,13h,15h,15ah,16h-oxacyclotetradeca[2,3-d]isoindol-2-one)