NP-MRD: Showing NP-Card for 1,10-Bis(dihydrocaffeoyl)spermine (NP0084549)

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Record Information

Version

2.0

Created at

2022-04-29 05:15:28 UTC

Updated at

2022-04-29 05:15:28 UTC

NP-MRD ID

NP0084549

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,10-Bis(dihydrocaffeoyl)spermine

Description

Kukoamine B belongs to the class of organic compounds known as catechols. Catechols are compounds containing a 1,2-benzenediol moiety. UK scientists at the Institute for Food Research have identified blood pressure-lowering compounds called kukoamines in potatoes. Kukoamine B is a very strong basic compound (based on its pKa). Kukoamine B (KB), a natural alkaloid compound with high affinity for both LPS and CpG DNA, was isolated from a traditional Chinese herb cortex Lycii. 1,10-Bis(dihydrocaffeoyl)spermine is found in Lycium chinense . Kukoamine B, a novel dual inhibitor of LPS and CpG DNA, is a potential candidate for sepsis treatment.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 06041318092D          

 38 39  0  0  0  0            999 V2000
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   14.2894  -12.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   13.5749  -10.3125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605   -9.9000    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


  Mrv0541 06041318092D          

 38 39  0  0  0  0            999 V2000
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   17.8618  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5762   -9.9000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8618  -11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5762  -11.5500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1473  -11.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328  -11.1375    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
  6  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
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 19 26  1  0  0  0  0
  5 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  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
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  2  0  0  0  0
 31 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084549

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCN(CCCCNCCCNC(=O)CCC1=CC=C(O)C(O)=C1)C(=O)CCC1=CC(O)=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C28H42N4O6/c29-13-3-18-32(28(38)12-8-22-6-10-24(34)26(36)20-22)17-2-1-14-30-15-4-16-31-27(37)11-7-21-5-9-23(33)25(35)19-21/h5-6,9-10,19-20,30,33-36H,1-4,7-8,11-18,29H2,(H,31,37)

> <INCHI_KEY>
IWRAOCFRRTWUDF-UHFFFAOYSA-N

> <FORMULA>
C28H42N4O6

> <MOLECULAR_WEIGHT>
530.6563

> <EXACT_MASS>
530.310435096

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
60.404091607921124

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[3-({4-[N-(3-aminopropyl)-3-(3,4-dihydroxyphenyl)propanamido]butyl}amino)propyl]-3-(3,4-dihydroxyphenyl)propanamide

> <ALOGPS_LOGP>
1.34

> <JCHEM_LOGP>
-0.35638553897922454

> <ALOGPS_LOGS>
-4.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
10.393733603437537

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.386510272987795

> <JCHEM_PKA_STRONGEST_BASIC>
9.84423762991696

> <JCHEM_POLAR_SURFACE_AREA>
168.38

> <JCHEM_REFRACTIVITY>
148.13729999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.74e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[3-({4-[N-(3-aminopropyl)-3-(3,4-dihydroxyphenyl)propanamido]butyl}amino)propyl]-3-(3,4-dihydroxyphenyl)propanamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-13         0                                  
HETATM    1  N   UNK     0      28.007 -23.870   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      26.674 -23.100   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      26.674 -21.560   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      25.340 -20.790   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      25.340 -19.250   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      24.006 -18.480   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.673 -19.250   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      21.339 -18.480   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      20.005 -19.250   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      18.672 -18.480   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      17.338 -19.250   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      16.004 -18.480   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.671 -19.250   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      13.337 -18.480   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      12.003 -19.250   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.003 -20.790   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      10.669 -18.480   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.336 -19.250   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002 -18.480   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668 -19.250   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335 -18.480   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335 -16.940   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       4.001 -16.170   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       6.668 -16.170   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       6.668 -14.630   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       8.002 -16.940   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      26.674 -18.480   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      26.674 -16.940   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      28.007 -19.250   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      29.341 -18.480   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      30.675 -19.250   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      32.008 -18.480   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      33.342 -19.250   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      34.676 -18.480   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      33.342 -20.790   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      34.676 -21.560   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      32.008 -21.560   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      30.675 -20.790   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   27                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   19                                                       
CONECT   27    5   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   38                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37   31                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₂N₄O₆

Average Mass

530.6563 Da

Monoisotopic Mass

530.31044 Da

IUPAC Name

N-[3-({4-[N-(3-aminopropyl)-3-(3,4-dihydroxyphenyl)propanamido]butyl}amino)propyl]-3-(3,4-dihydroxyphenyl)propanamide

Traditional Name

N-[3-({4-[N-(3-aminopropyl)-3-(3,4-dihydroxyphenyl)propanamido]butyl}amino)propyl]-3-(3,4-dihydroxyphenyl)propanamide

CAS Registry Number

Not Available

SMILES

NCCCN(CCCCNCCCNC(=O)CCC1=CC=C(O)C(O)=C1)C(=O)CCC1=CC(O)=C(O)C=C1

InChI Identifier

InChI=1S/C28H42N4O6/c29-13-3-18-32(28(38)12-8-22-6-10-24(34)26(36)20-22)17-2-1-14-30-15-4-16-31-27(37)11-7-21-5-9-23(33)25(35)19-21/h5-6,9-10,19-20,30,33-36H,1-4,7-8,11-18,29H2,(H,31,37)

InChI Key

IWRAOCFRRTWUDF-UHFFFAOYSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Lycium chinense	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as catechols. Catechols are compounds containing a 1,2-benzenediol moiety.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
Fatty acyl
Fatty amide
Tertiary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid derivative
Secondary amine
Secondary aliphatic amine
Amine
Organonitrogen compound
Primary aliphatic amine
Organooxygen compound
Primary amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

amine (CHEBI:81221 )

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	1.34	ALOGPS
logP	-0.36	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	9.39	ChemAxon
pKa (Strongest Basic)	9.84	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	168.38 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	148.14 m³·mol⁻¹	ChemAxon
Polarizability	60.4 Å³	ChemAxon
Number of Rings	2	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

HMDB ID

HMDB0060525

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C17616

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10346914

PDB ID

Not Available

ChEBI ID

81221

Good Scents ID

Not Available

References

General References

Showing NP-Card for 1,10-Bis(dihydrocaffeoyl)spermine (NP0084549)

MOL for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

3D MOL for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

3D SDF for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

3D-SDF for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

PDB for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

3D PDB for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

SMILES for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

INCHI for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

Structure for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)

3D Structure for NP0084549 (1,10-Bis(dihydrocaffeoyl)spermine)