NP-MRD: Showing NP-Card for (3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one (NP0319773)

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Record Information

Version

2.0

Created at

2022-09-11 20:58:49 UTC

Updated at

2022-09-11 20:58:49 UTC

NP-MRD ID

NP0319773

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one

Description

Phomacin C belongs to the class of organic compounds known as aspochalasins. These are cytochalasans with a structure in which the hydrogenated isoindole bears a 2-methylpropyl group. Phomacin C is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one was first documented in 2017 (PMID: 28931947). Based on a literature review a small amount of articles have been published on phomacin C (PMID: 33555630).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112222582D          

 30 32  0  0  1  0            999 V2000
   -0.5976   -1.0268    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0621   -1.5575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8256   -1.2450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4780   -1.7500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2979   -1.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6562   -0.6289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2684    0.1346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4737   -0.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6206   -1.5519    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4016   -1.0787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7101   -0.2599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3098   -2.1349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1987   -2.9524    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8666   -3.4953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4352   -3.2649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7828   -2.7600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0644   -2.9649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.9000   -3.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6919   -3.5638    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4660   -3.8987    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6646   -3.7027    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0408   -4.2982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.8847   -2.6398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
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 29 30  1  6  0  0  0
M  END

     RDKit          3D

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   -3.9096    0.8738   -0.3107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8836    1.0891    0.8027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2912    1.7342    2.0113 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652309112222582D          

 30 32  0  0  1  0            999 V2000
   -0.5976   -1.0268    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0319773

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C[C@@H]1N=C(O)[C@]23[C@H]1[C@H](C)C(C)=C[C@@H]2\C=C(C)\C[C@H](CO)C[C@H](O)\C=C\C3=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H37NO4/c1-14(2)8-21-23-17(5)16(4)11-19-10-15(3)9-18(13-27)12-20(28)6-7-22(29)25(19,23)24(30)26-21/h6-7,10-11,14,17-21,23,27-28H,8-9,12-13H2,1-5H3,(H,26,30)/b7-6+,15-10+/t17-,18+,19+,20-,21+,23+,25-/m1/s1

> <INCHI_KEY>
AQAFUDMWTUOKSI-USVVNQICSA-N

> <FORMULA>
C25H37NO4

> <MOLECULAR_WEIGHT>
415.574

> <EXACT_MASS>
415.272258675

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
47.60173956936619

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,4S,6aS,10S,12S,15aR,15bR)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3H,4H,6aH,9H,10H,11H,12H,15H,15bH-cycloundeca[e]isoindol-15-one

> <JCHEM_LOGP>
2.4931637200754104

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.74578004465386

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8786910737478104

> <JCHEM_PKA_STRONGEST_BASIC>
5.699128920035266

> <JCHEM_POLAR_SURFACE_AREA>
90.12

> <JCHEM_REFRACTIVITY>
121.82039999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S,6aS,10S,12S,15aR,15bR)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3H,4H,6aH,9H,10H,11H,12H,15bH-cycloundeca[e]isoindol-15-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.116  -1.917   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.116  -2.907   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.541  -2.324   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.759  -3.267   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.289  -2.561   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.958  -1.174   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.234   0.251   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.484  -1.381   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.758  -2.897   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.216  -2.013   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       8.792  -0.485   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       8.045  -3.985   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.838  -5.511   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.084  -6.524   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.412  -6.095   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.195  -5.152   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.853  -5.534   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.912  -7.443   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.551  -4.793   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.547  -5.968   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.025  -6.652   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0       2.737  -7.278   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       1.241  -6.912   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.076  -8.023   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.123  -9.587   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.479 -10.316   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.187 -10.396   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.126  -5.376   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.092  -4.433   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.651  -4.928   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   29                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   19                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    4   20   28                                             
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   23   19   29                                                  
CONECT   29   28    2   30                                                  
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₇NO₄

Average Mass

415.5740 Da

Monoisotopic Mass

415.27226 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)C[C@@H]1N=C(O)[C@]23[C@H]1[C@H](C)C(C)=C[C@@H]2\C=C(C)\C[C@H](CO)C[C@H](O)\C=C\C3=O

InChI Identifier

InChI=1S/C25H37NO4/c1-14(2)8-21-23-17(5)16(4)11-19-10-15(3)9-18(13-27)12-20(28)6-7-22(29)25(19,23)24(30)26-21/h6-7,10-11,14,17-21,23,27-28H,8-9,12-13H2,1-5H3,(H,26,30)/b7-6+,15-10+/t17-,18+,19+,20-,21+,23+,25-/m1/s1

InChI Key

AQAFUDMWTUOKSI-USVVNQICSA-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 aspochalasins. These are cytochalasans with a structure in which the hydrogenated isoindole bears a 2-methylpropyl group.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Cytochalasans

Sub Class

Aspochalasins

Direct Parent

Aspochalasins

Alternative Parents

Substituents

Aspochalasin skeleton
Carbocyclic aspochalasin skeleton
Isoindolone
Isoindoline
Isoindole
Isoindole or derivatives
2-pyrrolidone
Pyrrolidone
Pyrrolidine
Carboxamide group
Ketone
Secondary carboxylic acid amide
Secondary alcohol
Lactam
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Primary alcohol
Organonitrogen compound
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

organic heterotricyclic compound (CHEBI:66748 )
macrocycle (CHEBI:66748 )
cytochalasin (CHEBI:66748 )

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00043815

Chemspider ID

8223049

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10047486

PDB ID

Not Available

ChEBI ID

66748

Good Scents ID

Not Available

References

General References

Sallam A, Sabry MA, Galala AA: Westalsan: A New Acetylcholine Esterase Inhibitor from the Endophytic Fungus Westerdykella nigra. Chem Biodivers. 2021 Apr;18(4):e2000957. doi: 10.1002/cbdv.202000957. Epub 2021 Mar 3. [PubMed:33555630 ]
Xu D, Luo M, Liu F, Wang D, Pang X, Zhao T, Xu L, Wu X, Xia M, Yang X: Cytochalasan and Tyrosine-Derived Alkaloids from the Marine Sediment-Derived Fungus Westerdykella dispersa and Their Bioactivities. Sci Rep. 2017 Sep 20;7(1):11956. doi: 10.1038/s41598-017-12327-1. [PubMed:28931947 ]
LOTUS database [Link]

Showing NP-Card for (3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one (NP0319773)

MOL for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

3D MOL for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

3D SDF for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

3D-SDF for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

PDB for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

3D PDB for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

SMILES for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

INCHI for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

Structure for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)

3D Structure for NP0319773 ((3s,3ar,4s,6as,10s,12s,15ar)-1,12-dihydroxy-10-(hydroxymethyl)-4,5,8-trimethyl-3-(2-methylpropyl)-3h,3ah,4h,6ah,9h,10h,11h,12h-cycloundeca[d]isoindol-15-one)