NP-MRD: Showing NP-Card for microsphaerin D (NP0037737)

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Record Information

Version

2.0

Created at

2021-06-20 20:35:35 UTC

Updated at

2021-06-30 00:10:07 UTC

NP-MRD ID

NP0037737

Secondary Accession Numbers

None

Natural Product Identification

Common Name

microsphaerin D

Provided By

JEOL Database JEOL Logo

Description

microsphaerin D is found in Microsphaeropsis sp. microsphaerin D was first documented in 2008 (Yoganathan, K., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202122353D          

 66 71  0  0  0  0            999 V2000
    0.8769    7.5906   -3.8483 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5052    6.4441   -2.9551 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5030    6.6051   -1.5658 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1264    5.5495   -0.7357 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1377    5.8122    0.6110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441    4.3053   -1.2702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5993    3.2067   -0.3338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0259    3.4886    0.7885 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.9070    1.4037   -0.3036 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0053   -0.2365   -2.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 66 71  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652306202122353D          

 66 71  0  0  0  0            999 V2000
    0.8769    7.5906   -3.8483 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5052    6.4441   -2.9551 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5030    6.6051   -1.5658 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1264    5.5495   -0.7357 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1377    5.8122    0.6110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441    4.3053   -1.2702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5993    3.2067   -0.3338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0259    3.4886    0.7885 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4174    1.7799   -0.6815 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0037737

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C(=C([H])C(O[H])=C1C(=O)C1=C(O[H])C2=C(C(O[H])=C1C([H])([H])[H])[C@@]1(O[H])C([H])([H])[C@]2([H])C(O[H])=C2C(=O)C3=C(O[H])C([H])=C(C([H])=C3O[C@@]12C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C30H26O10/c1-10-5-14(31)20(15(32)6-10)27(37)18-12(3)24(34)22-19(26(18)36)13-9-30(22,39)29(4)23(25(13)35)28(38)21-16(33)7-11(2)8-17(21)40-29/h5-8,13,31-36,39H,9H2,1-4H3/t13-,29+,30-/m0/s1

> <INCHI_KEY>
HMNKFQXCRPMHBY-XFNOWFNXSA-N

> <FORMULA>
C30H26O10

> <MOLECULAR_WEIGHT>
546.528

> <EXACT_MASS>
546.152597037

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
55.16836643940049

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,13S)-16-(2,6-dihydroxy-4-methylbenzoyl)-1,8,12,15,18-pentahydroxy-2,6,17-trimethyl-3-oxapentacyclo[11.6.1.0^{2,11}.0^{4,9}.0^{14,19}]icosa-4,6,8,11,14(19),15,17-heptaen-10-one

> <ALOGPS_LOGP>
2.68

> <JCHEM_LOGP>
6.259360102333334

> <ALOGPS_LOGS>
-3.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.412926919533445

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.825873903612147

> <JCHEM_PKA_STRONGEST_BASIC>
-3.858113586808952

> <JCHEM_POLAR_SURFACE_AREA>
184.98

> <JCHEM_REFRACTIVITY>
144.9167

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.34e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,13S)-16-(2,6-dihydroxy-4-methylbenzoyl)-1,8,12,15,18-pentahydroxy-2,6,17-trimethyl-3-oxapentacyclo[11.6.1.0^{2,11}.0^{4,9}.0^{14,19}]icosa-4,6,8,11,14(19),15,17-heptaen-10-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 66 71  0  0  0  0  0  0  0  0999 V2000
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M  END

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0       0.877   7.591  -3.848  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.505   6.444  -2.955  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.503   6.605  -1.566  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.126   5.550  -0.736  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.138   5.812   0.611  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.244   4.305  -1.270  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.599   3.207  -0.334  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.026   3.489   0.789  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.417   1.780  -0.682  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.528   0.888  -0.623  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.907   1.404  -0.304  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.298  -0.480  -0.842  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.271  -1.431  -0.746  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.029  -0.915  -1.179  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.047  -0.014  -1.279  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.876   1.323  -0.984  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.946   2.166  -0.946  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.300  -0.789  -1.616  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.653  -1.955  -2.383  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.482  -2.326  -1.445  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.466  -3.121  -2.141  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.068  -3.034  -0.146  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.432  -4.500  -0.493  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.022  -3.074   0.853  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.418  -3.392   2.125  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.580  -3.889   2.966  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.279  -4.265   4.283  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.357  -4.777   5.192  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.029  -4.101   4.757  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.020  -3.585   3.925  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.266  -3.445   4.473  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.718  -3.229   2.607  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.736  -2.628   1.732  0.00  0.00           C+0
HETATM   34  O   UNK     0       3.871  -2.383   2.132  0.00  0.00           O+0
HETATM   35  C   UNK     0       2.296  -2.289   0.366  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.899  -1.290  -0.317  0.00  0.00           C+0
HETATM   37  O   UNK     0       3.992  -0.580   0.133  0.00  0.00           O+0
HETATM   38  C   UNK     0      -0.286   4.163  -2.664  0.00  0.00           C+0
HETATM   39  O   UNK     0      -0.734   3.003  -3.236  0.00  0.00           O+0
HETATM   40  C   UNK     0       0.089   5.222  -3.500  0.00  0.00           C+0
HETATM   41  H   UNK     0       1.616   8.239  -3.366  0.00  0.00           H+0
HETATM   42  H   UNK     0      -0.012   8.183  -4.086  0.00  0.00           H+0
HETATM   43  H   UNK     0       1.322   7.230  -4.781  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.790   7.554  -1.117  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.285   5.046   1.062  0.00  0.00           H+0
HETATM   46  H   UNK     0      -3.678   0.808  -0.803  0.00  0.00           H+0
HETATM   47  H   UNK     0      -3.078   1.373   0.777  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.053   2.427  -0.663  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.000  -1.076  -0.209  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.756   1.643  -0.800  0.00  0.00           H+0
HETATM   51  H   UNK     0       3.005  -0.237  -2.242  0.00  0.00           H+0
HETATM   52  H   UNK     0       2.344  -2.782  -2.576  0.00  0.00           H+0
HETATM   53  H   UNK     0       1.281  -1.630  -3.366  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.343  -2.844  -1.802  0.00  0.00           H+0
HETATM   55  H   UNK     0       2.169  -4.569  -1.298  0.00  0.00           H+0
HETATM   56  H   UNK     0       1.847  -5.036   0.368  0.00  0.00           H+0
HETATM   57  H   UNK     0       0.540  -5.064  -0.789  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.594  -3.994   2.586  0.00  0.00           H+0
HETATM   59  H   UNK     0      -1.830  -3.942   5.718  0.00  0.00           H+0
HETATM   60  H   UNK     0      -2.121  -5.318   4.625  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.946  -5.474   5.931  0.00  0.00           H+0
HETATM   62  H   UNK     0       1.282  -4.366   5.782  0.00  0.00           H+0
HETATM   63  H   UNK     0       3.853  -3.025   3.807  0.00  0.00           H+0
HETATM   64  H   UNK     0       4.323  -1.010   0.955  0.00  0.00           H+0
HETATM   65  H   UNK     0      -0.629   3.059  -4.200  0.00  0.00           H+0
HETATM   66  H   UNK     0       0.051   5.111  -4.580  0.00  0.00           H+0
CONECT    1    2   41   42   43                                             
CONECT    2    3   40    1                                                  
CONECT    3    4    2   44                                                  
CONECT    4    6    3    5                                                  
CONECT    5    4   45                                                       
CONECT    6    4   38    7                                                  
CONECT    7    8    9    6                                                  
CONECT    8    7                                                            
CONECT    9   16   10    7                                                  
CONECT   10   12    9   11                                                  
CONECT   11   10   46   47   48                                             
CONECT   12   14   10   13                                                  
CONECT   13   12   49                                                       
CONECT   14   15   20   12                                                  
CONECT   15   14   18   16                                                  
CONECT   16   15    9   17                                                  
CONECT   17   16   50                                                       
CONECT   18   15   36   19   51                                             
CONECT   19   18   20   52   53                                             
CONECT   20   14   22   21   19                                             
CONECT   21   20   54                                                       
CONECT   22   35   20   24   23                                             
CONECT   23   22   55   56   57                                             
CONECT   24   22   25                                                       
CONECT   25   26   32   24                                                  
CONECT   26   27   25   58                                                  
CONECT   27   29   26   28                                                  
CONECT   28   27   59   60   61                                             
CONECT   29   30   27   62                                                  
CONECT   30   29   32   31                                                  
CONECT   31   30   63                                                       
CONECT   32   33   25   30                                                  
CONECT   33   34   35   32                                                  
CONECT   34   33                                                            
CONECT   35   22   36   33                                                  
CONECT   36   35   18   37                                                  
CONECT   37   36   64                                                       
CONECT   38   40    6   39                                                  
CONECT   39   38   65                                                       
CONECT   40    2   38   66                                                  
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    3                                                            
CONECT   45    5                                                            
CONECT   46   11                                                            
CONECT   47   11                                                            
CONECT   48   11                                                            
CONECT   49   13                                                            
CONECT   50   17                                                            
CONECT   51   18                                                            
CONECT   52   19                                                            
CONECT   53   19                                                            
CONECT   54   21                                                            
CONECT   55   23                                                            
CONECT   56   23                                                            
CONECT   57   23                                                            
CONECT   58   26                                                            
CONECT   59   28                                                            
CONECT   60   28                                                            
CONECT   61   28                                                            
CONECT   62   29                                                            
CONECT   63   31                                                            
CONECT   64   37                                                            
CONECT   65   39                                                            
CONECT   66   40                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  142    0
END

RDKit          3D

66 71  0  0  0  0  0  0  0  0999 V2000
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    3.8533   -3.0253    3.8067 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3226   -1.0103    0.9548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6287    3.0594   -4.1999 H   0  0  0  0  0  0  0  0  0  0  0  0
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 28 59  1  0
 28 60  1  0
 28 61  1  0
 31 63  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₆O₁₀

Average Mass

546.5280 Da

Monoisotopic Mass

546.15260 Da

IUPAC Name

(1S,2R,13S)-16-(2,6-dihydroxy-4-methylbenzoyl)-1,8,12,15,18-pentahydroxy-2,6,17-trimethyl-3-oxapentacyclo[11.6.1.0^{2,11}.0^{4,9}.0^{14,19}]icosa-4,6,8,11,14(19),15,17-heptaen-10-one

Traditional Name

(1S,2R,13S)-16-(2,6-dihydroxy-4-methylbenzoyl)-1,8,12,15,18-pentahydroxy-2,6,17-trimethyl-3-oxapentacyclo[11.6.1.0^{2,11}.0^{4,9}.0^{14,19}]icosa-4,6,8,11,14(19),15,17-heptaen-10-one

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C(=C([H])C(O[H])=C1C(=O)C1=C(O[H])C2=C(C(O[H])=C1C([H])([H])[H])[C@@]1(O[H])C([H])([H])[C@]2([H])C(O[H])=C2C(=O)C3=C(O[H])C([H])=C(C([H])=C3O[C@@]12C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]

InChI Identifier

InChI=1S/C30H26O10/c1-10-5-14(31)20(15(32)6-10)27(37)18-12(3)24(34)22-19(26(18)36)13-9-30(22,39)29(4)23(25(13)35)28(38)21-16(33)7-11(2)8-17(21)40-29/h5-8,13,31-36,39H,9H2,1-4H3/t13-,29+,30-/m0/s1

InChI Key

HMNKFQXCRPMHBY-XFNOWFNXSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Microsphaeropsis sp.	JEOL database	Yoganathan, K., et al, Tetrahedron 64, 10181 (2008)

Chemical Taxonomy

Classification

Not classified

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	2.68	ALOGPS
logP	6.26	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	6.83	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	184.98 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	144.92 m³·mol⁻¹	ChemAxon
Polarizability	55.17 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Yoganathan, K., et al. (2008). Yoganathan, K., et al, Tetrahedron 64, 10181 (2008). Tetrahedron.

Showing NP-Card for microsphaerin D (NP0037737)

MOL for NP0037737 (microsphaerin D)

3D MOL for NP0037737 (microsphaerin D)

3D SDF for NP0037737 (microsphaerin D)

3D-SDF for NP0037737 (microsphaerin D)

PDB for NP0037737 (microsphaerin D)

3D PDB for NP0037737 (microsphaerin D)

SMILES for NP0037737 (microsphaerin D)

INCHI for NP0037737 (microsphaerin D)

Structure for NP0037737 (microsphaerin D)

3D Structure for NP0037737 (microsphaerin D)