NP-MRD: Showing NP-Card for (+)-Spongidine B (NP0081185)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-29 02:09:08 UTC

Updated at

2022-04-29 02:09:08 UTC

NP-MRD ID

NP0081185

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Spongidine B

Description

(+)-Spongidine B is found in Spongia sp.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292204092D          

 30 33  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  2  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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1758    1.5039    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
    3.8679    2.3042    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7404    3.1193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3825    3.6373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9708    3.4164    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  2  0  0  0  0
 20 22  1  0  0  0  0
  8 23  1  1  0  0  0
  5 24  1  1  0  0  0
  3 25  1  6  0  0  0
  3 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
M  END


  Mrv1652304292204092D          

 30 33  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  2  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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1758    1.5039    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
    3.8679    2.3042    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7404    3.1193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3825    3.6373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9708    3.4164    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  2  0  0  0  0
 20 22  1  0  0  0  0
  8 23  1  1  0  0  0
  5 24  1  1  0  0  0
  3 25  1  6  0  0  0
  3 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0081185

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C25H36NO4/c1-17(27)30-16-23(2)10-5-11-25(4)20(23)8-12-24(3)19-9-13-26(15-22(28)29)14-18(19)6-7-21(24)25/h9,13-14,20-21H,5-8,10-12,15-16H2,1-4H3,(H,28,29)/t20-,21-,23+,24-,25-/m0/s1

> <INCHI_KEY>
YKXZFFKYOZDVNS-XPVPTZRYSA-N

> <FORMULA>
C25H36NO4

> <MOLECULAR_WEIGHT>
414.566

> <EXACT_MASS>
414.264433643

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
48.04036414121817

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <ALOGPS_LOGP>
5.04

> <JCHEM_LOGP>
4.882331761333335

> <ALOGPS_LOGS>
-5.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.232834173812118

> <JCHEM_PKA_STRONGEST_BASIC>
-6.995029951302066

> <JCHEM_POLAR_SURFACE_AREA>
68.53

> <JCHEM_REFRACTIVITY>
115.51739999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.02e-04 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  O   UNK     0      -4.211   1.061   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -2.195   2.807   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.350   2.516   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.375  -0.976   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.023   3.273   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.657   3.747   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       7.220   4.301   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.982   5.823   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       8.181   6.790   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       5.545   6.377   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   25   26                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   24                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9   11   23                                             
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   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23    8                                                            
CONECT   24    5                                                            
CONECT   25    3                                                            
CONECT   26    3   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₆NO₄

Average Mass

414.5660 Da

Monoisotopic Mass

414.26443 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C25H36NO4/c1-17(27)30-16-23(2)10-5-11-25(4)20(23)8-12-24(3)19-9-13-26(15-22(28)29)14-18(19)6-7-21(24)25/h9,13-14,20-21H,5-8,10-12,15-16H2,1-4H3,(H,28,29)/t20-,21-,23+,24-,25-/m0/s1

InChI Key

YKXZFFKYOZDVNS-XPVPTZRYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Spongia sp.	-	KNApSAcK

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	5.04	ALOGPS
logP	4.88	ChemAxon
logS	-5.9	ALOGPS
pKa (Strongest Acidic)	4.23	ChemAxon
pKa (Strongest Basic)	-7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	68.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	115.52 m³·mol⁻¹	ChemAxon
Polarizability	48.04 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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 B (NP0081185)

MOL for NP0081185 ((+)-Spongidine B)

3D MOL for NP0081185 ((+)-Spongidine B)

3D SDF for NP0081185 ((+)-Spongidine B)

3D-SDF for NP0081185 ((+)-Spongidine B)

PDB for NP0081185 ((+)-Spongidine B)

3D PDB for NP0081185 ((+)-Spongidine B)

SMILES for NP0081185 ((+)-Spongidine B)

INCHI for NP0081185 ((+)-Spongidine B)

Structure for NP0081185 ((+)-Spongidine B)

3D Structure for NP0081185 ((+)-Spongidine B)