NP-MRD: Showing NP-Card for (2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid (NP0325872)

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Record Information

Version

2.0

Created at

2022-09-12 06:57:48 UTC

Updated at

2022-09-12 06:57:48 UTC

NP-MRD ID

NP0325872

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid

Description

Psymberin, also known as irciniastatin a, belongs to the class of organic compounds known as hydroxybenzoic acid derivatives. Hydroxybenzoic acid derivatives are compounds containing a hydroxybenzoic acid (or a derivative), which is a benzene ring bearing a carboxyl and a hydroxyl groups. (2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid is found in Ircinia ramosa and Psammocinia bulbosa. (2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid was first documented in 2013 (PMID: 25110364). Based on a literature review a small amount of articles have been published on Psymberin (PMID: 31063392) (PMID: 26544018) (PMID: 24105772) (PMID: 23606588).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122208572D          

 43 45  0  0  1  0            999 V2000
    5.7158   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309122208572D          

 43 45  0  0  1  0            999 V2000
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    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.8592   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.5737   -7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -6.1875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.4315   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.0026   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2881   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1868   -3.0805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2474   -3.0805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.1460   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.8605   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.5749   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.0039   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1473   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8618   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1473   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -4.9500    0.0000 O   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  4  0  0  0
 10 12  2  0  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 16 13  1  6  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 27 28  1  1  0  0  0
 29 27  1  1  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 37 39  2  0  0  0  0
 31 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  2  0  0  0  0
 40 42  1  0  0  0  0
 29 42  1  0  0  0  0
 23 43  1  0  0  0  0
 16 43  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0325872

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H](CC(C)=C)[C@H](O)C(O)=N[C@@H](OC)[C@@H]1C[C@@H](O)C(C)(C)[C@@H](C[C@H](O)[C@@H](C)[C@H]2CC3=C(C)C(O)=CC(O)=C3C(=O)O2)O1

> <INCHI_IDENTIFIER>
InChI=1S/C31H47NO11/c1-14(2)9-22(40-7)27(37)28(38)32-29(41-8)23-13-24(36)31(5,6)25(42-23)12-19(34)16(4)21-10-17-15(3)18(33)11-20(35)26(17)30(39)43-21/h11,16,19,21-25,27,29,33-37H,1,9-10,12-13H2,2-8H3,(H,32,38)/t16-,19+,21-,22+,23+,24-,25-,27+,29+/m1/s1

> <INCHI_KEY>
BNNIEBYABSNREN-CYRUSRGFSA-N

> <FORMULA>
C31H47NO11

> <MOLECULAR_WEIGHT>
609.713

> <EXACT_MASS>
609.314911337

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
90

> <JCHEM_AVERAGE_POLARIZABILITY>
64.69801392118595

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S)-N-[(S)-[(2S,4R,6R)-6-[(2S,3R)-3-[(3R)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-1H-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid

> <JCHEM_LOGP>
3.555012151000001

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.84172412193387

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4001068958124288

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2769442736523833

> <JCHEM_POLAR_SURFACE_AREA>
187.72999999999996

> <JCHEM_REFRACTIVITY>
157.10060000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S)-N-[(S)-[(2S,4R,6R)-6-[(2S,3R)-3-[(3R)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.003 -11.550   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.337 -12.320   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.670 -11.550   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      14.670 -10.010   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      16.004  -9.240   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.004 -12.320   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      16.004 -13.860   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      17.338 -11.550   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      17.338 -10.010   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      18.672 -12.320   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      20.005 -11.550   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      21.339 -12.320   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      22.673 -11.550   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      20.005 -10.010   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      18.672  -9.240   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      18.672  -7.700   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      17.338  -6.930   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      20.005  -6.930   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      19.015  -5.750   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      20.995  -5.750   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      21.339  -7.700   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      22.673  -6.930   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      24.006  -7.700   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      24.006  -9.240   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      25.340  -6.930   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      25.340  -5.390   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      26.674  -7.700   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      28.007  -6.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      29.341  -7.700   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      30.675  -6.930   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      30.675  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      32.008  -7.700   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      33.342  -6.930   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      32.008  -9.240   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      30.675 -10.010   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      30.675 -11.550   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      29.341  -9.240   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      28.007 -10.010   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      28.007 -11.550   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      26.674  -9.240   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      21.339  -9.240   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   43                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20   24   43                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   42                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32   39                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   31   40                                                  
CONECT   40   39   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40   29                                                       
CONECT   43   23   16                                                       
MASTER        0    0    0    0    0    0    0    0   43    0   90    0
END

View in JSmol

Synonyms

Value	Source
Irciniastatin a	MeSH

Chemical Formula

C₃₁H₄₇NO₁₁

Average Mass

609.7130 Da

Monoisotopic Mass

609.31491 Da

IUPAC Name

(2S,3S)-N-[(S)-[(2S,4R,6R)-6-[(2S,3R)-3-[(3R)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-1H-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid

Traditional Name

(2S,3S)-N-[(S)-[(2S,4R,6R)-6-[(2S,3R)-3-[(3R)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid

CAS Registry Number

Not Available

SMILES

CO[C@@H](CC(C)=C)[C@H](O)C(O)=N[C@@H](OC)[C@@H]1C[C@@H](O)C(C)(C)[C@@H](C[C@H](O)[C@@H](C)[C@H]2CC3=C(C)C(O)=CC(O)=C3C(=O)O2)O1

InChI Identifier

InChI=1S/C31H47NO11/c1-14(2)9-22(40-7)27(37)28(38)32-29(41-8)23-13-24(36)31(5,6)25(42-23)12-19(34)16(4)21-10-17-15(3)18(33)11-20(35)26(17)30(39)43-21/h11,16,19,21-25,27,29,33-37H,1,9-10,12-13H2,2-8H3,(H,32,38)/t16-,19+,21-,22+,23+,24-,25-,27+,29+/m1/s1

InChI Key

BNNIEBYABSNREN-CYRUSRGFSA-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
Ircinia ramosa	LOTUS Database	35616633
Psammocinia bulbosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxybenzoic acid derivatives. Hydroxybenzoic acid derivatives are compounds containing a hydroxybenzoic acid (or a derivative), which is a benzene ring bearing a carboxyl and a hydroxyl groups.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Hydroxybenzoic acid derivatives

Alternative Parents

Substituents

Dihydroxybenzoic acid
Benzopyran
Isochromane
2-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Fatty amide
Fatty acyl
Oxane
Monosaccharide
N-acyl-amine
Vinylogous acid
Carboxamide group
Carboxylic acid ester
Lactone
Secondary carboxylic acid amide
Secondary alcohol
Carboxylic acid derivative
Dialkyl ether
Ether
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organic oxide
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organopnictogen compound
Organooxygen compound
Organonitrogen 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	3.56	ChemAxon
pKa (Strongest Acidic)	3.4	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	187.73 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	157.1 m³·mol⁻¹	ChemAxon
Polarizability	64.7 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00038085

Chemspider ID

9867673

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Psymberin

METLIN ID

Not Available

PubChem Compound

11692946

PDB ID

Not Available

ChEBI ID

182709

Good Scents ID

Not Available

References

General References

Yu J, Yang M, Guo Y, Ye T: Total Synthesis of Psymberin (Irciniastatin A). Org Lett. 2019 May 17;21(10):3670-3673. doi: 10.1021/acs.orglett.9b01113. Epub 2019 May 7. [PubMed:31063392 ]
Uesugi S, Watanabe T, Imaizumi T, Ota Y, Yoshida K, Ebisu H, Chinen T, Nagumo Y, Shibuya M, Kanoh N, Usui T, Iwabuchi Y: Total Synthesis and Biological Evaluation of Irciniastatin A (a.k.a. Psymberin) and Irciniastatin B. J Org Chem. 2015 Dec 18;80(24):12333-50. doi: 10.1021/acs.joc.5b02256. Epub 2015 Nov 16. [PubMed:26544018 ]
Pal A, Peng Z, Schuber PT Jr, Bhanu Prasad BA, Bornmann WG: Asymmetric Synthesis of the C1-C6 Portion of the Psymberin Using an Evans Chiral Auxiliary. Tetrahedron Lett. 2013 Oct 9;54(41):5555-5567. doi: 10.1016/j.tetlet.2013.05.153. [PubMed:25110364 ]
Bielitza M, Pietruszka J: The psymberin story--biological properties and approaches towards total and analogue syntheses. Angew Chem Int Ed Engl. 2013 Oct 11;52(42):10960-85. doi: 10.1002/anie.201301259. Epub 2013 Sep 17. [PubMed:24105772 ]
Bielitza M, Pietruszka J: Synthesis of 8-desmethoxy psymberin: a putative biosynthetic intermediate towards the marine polyketide psymberin. Chemistry. 2013 Jun 17;19(25):8300-8. doi: 10.1002/chem.201203149. Epub 2013 Apr 19. [PubMed:23606588 ]
LOTUS database [Link]

Showing NP-Card for (2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid (NP0325872)

MOL for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

3D MOL for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

3D SDF for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

3D-SDF for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

PDB for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

3D PDB for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

SMILES for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

INCHI for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

Structure for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)

3D Structure for NP0325872 ((2s,3s)-n-[(s)-[(2s,4r,6r)-6-[(2s,3r)-3-[(3r)-6,8-dihydroxy-5-methyl-1-oxo-3,4-dihydro-2-benzopyran-3-yl]-2-hydroxybutyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-3-methoxy-5-methylhex-5-enimidic acid)