NP-MRD: Showing NP-Card for (-)-Spongidine D (NP0081186)

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Record Information

Version

2.0

Created at

2022-04-29 02:09:19 UTC

Updated at

2022-04-29 02:09:19 UTC

NP-MRD ID

NP0081186

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Spongidine D

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292204092D          

 28 31  0  0  1  0            999 V2000
    5.0352   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7651    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    1.0361    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6850    0.2566    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2251   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    0.1007    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3347    0.7243    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6048    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5246    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    0.2566    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9845    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9058    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4459    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2560    0.5684    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0662    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4119    1.3785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1001   -0.2417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946    1.3480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149   -0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3696    1.7536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6376    2.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  1  0  0  0
  8 11  1  0  0  0  0
 11 12  4  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  1  0  0  0
 12 15  4  0  0  0  0
 15 16  4  0  0  0  0
 16 17  4  0  0  0  0
 17 18  4  0  0  0  0
 11 18  4  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  2  0  0  0  0
 21 24  1  0  0  0  0
  8 25  1  1  0  0  0
  5 26  1  1  0  0  0
  3 27  1  0  0  0  0
  3 28  1  0  0  0  0
M  END


  Mrv1652304292204092D          

 28 31  0  0  1  0            999 V2000
    5.0352   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7651    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    1.0361    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6850    0.2566    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2251   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    0.1007    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3347    0.7243    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6048    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5246    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    0.2566    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9845    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9058    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4459    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2560    0.5684    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0662    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4119    1.3785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1001   -0.2417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946    1.3480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149   -0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3696    1.7536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6376    2.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  1  0  0  0
  8 11  1  0  0  0  0
 11 12  4  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  1  0  0  0
 12 15  4  0  0  0  0
 15 16  4  0  0  0  0
 16 17  4  0  0  0  0
 17 18  4  0  0  0  0
 11 18  4  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  2  0  0  0  0
 21 24  1  0  0  0  0
  8 25  1  1  0  0  0
  5 26  1  1  0  0  0
  3 27  1  0  0  0  0
  3 28  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0081186

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)CCC[C@@]2(C)[C@H]1CC[C@]1(C)[C@@H]2CCc2cn(CCS(O)(=O)=O)ccc12

> <INCHI_IDENTIFIER>
InChI=1S/C23H36NO3S/c1-21(2)10-5-11-23(4)19(21)8-12-22(3)18-9-13-24(14-15-28(25,26)27)16-17(18)6-7-20(22)23/h9,13,16,19-20H,5-8,10-12,14-15H2,1-4H3,(H,25,26,27)/t19-,20-,22-,23-/m0/s1

> <INCHI_KEY>
DKETWRMWEHPURL-SQOUVECCSA-N

> <FORMULA>
C23H36NO3S

> <MOLECULAR_WEIGHT>
406.61

> <EXACT_MASS>
406.241590197

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
47.07274023969107

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <ALOGPS_LOGP>
3.21

> <JCHEM_LOGP>
5.264284904666668

> <ALOGPS_LOGS>
-5.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.6340334009885824

> <JCHEM_POLAR_SURFACE_AREA>
59.3

> <JCHEM_REFRACTIVITY>
113.19289999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.05e-03 g/l

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.862   2.807   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.375   3.098   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.342  -0.394   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.350  -1.558   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.862  -1.267   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -0.179   0.479   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.691   0.188   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.699   1.352   0.000  0.00  0.00           C+0
HETATM   21  S   UNK     0      -4.211   1.061   0.000  0.00  0.00           S+0
HETATM   22  O   UNK     0      -5.723   0.770   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -4.502   2.573   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -3.920  -0.451   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       3.350   2.516   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.375  -0.976   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.023   3.273   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.657   3.747   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   27   28                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   26                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9   11   25                                             
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   18                                                  
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13    7                                                       
CONECT   15   12   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17   11                                                       
CONECT   19   16   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21                                                            
CONECT   25    8                                                            
CONECT   26    5                                                            
CONECT   27    3                                                            
CONECT   28    3                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   62    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₃₆NO₃S

Average Mass

406.6100 Da

Monoisotopic Mass

406.24159 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC1(C)CCC[C@@]2(C)[C@H]1CC[C@]1(C)[C@@H]2CCc2cn(CCS(O)(=O)=O)ccc12

InChI Identifier

InChI=1S/C23H36NO3S/c1-21(2)10-5-11-23(4)19(21)8-12-22(3)18-9-13-24(14-15-28(25,26)27)16-17(18)6-7-20(22)23/h9,13,16,19-20H,5-8,10-12,14-15H2,1-4H3,(H,25,26,27)/t19-,20-,22-,23-/m0/s1

InChI Key

DKETWRMWEHPURL-SQOUVECCSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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	3.21	ALOGPS
logP	5.26	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	-0.63	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	59.3 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	113.19 m³·mol⁻¹	ChemAxon
Polarizability	47.07 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Spongidine D (NP0081186)

MOL for NP0081186 ((-)-Spongidine D)

3D MOL for NP0081186 ((-)-Spongidine D)

3D SDF for NP0081186 ((-)-Spongidine D)

3D-SDF for NP0081186 ((-)-Spongidine D)

PDB for NP0081186 ((-)-Spongidine D)

3D PDB for NP0081186 ((-)-Spongidine D)

SMILES for NP0081186 ((-)-Spongidine D)

INCHI for NP0081186 ((-)-Spongidine D)

Structure for NP0081186 ((-)-Spongidine D)

3D Structure for NP0081186 ((-)-Spongidine D)