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Showing NP-Card for Dehydrospermidine (NP0339119)

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Record Information
Version2.0
Created at2024-09-11 19:46:40 UTC
Updated at2024-09-11 19:46:40 UTC
NP-MRD IDNP0339119
Secondary Accession NumbersNone
Natural Product Identification
Common NameDehydrospermidine
DescriptionDehydrospermidine belongs to the class of organic compounds known as shiff bases. These are aldimines where the nitrogen atom of the aldimine group is linked to an alkyl or aryl group. Dehydrospermidine is a very strong basic compound (based on its pKa). Outside of the human body, Dehydrospermidine has been detected, but not quantified in, several different foods, such as purple lavers, jackfruits, chinese cabbages, tea leaf willows, and wax gourds. This could make dehydrospermidine a potential biomarker for the consumption of these foods. Spermidine has also been found to reduce the amount of ageing in yeast, flies, worms and human immune cells by inducing autophagy. Spermidine is a polyamine involved in cellular metabolism that can be used to stimulate the enzyme, T7 RNA polymerase, a type of RNA polymerase. Dehydrospermidine is the reduction form of spermidine.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339119 (Dehydrospermidine)


  Mrv1652303102016472D          

 10  9  0  0  0  0            999 V2000
   11.1540  -15.1286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9790  -15.1286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3914  -14.4141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2164  -14.4141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6289  -13.6995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4538  -13.6995    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.8662  -12.9856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6912  -12.9856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1037  -12.2711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9287  -12.2711    0.0000 N   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  2  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
M  END
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3D MOL for NP0339119 (Dehydrospermidine)

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3D SDF for NP0339119 (Dehydrospermidine)

  Mrv1652303102016472D          

 10  9  0  0  0  0            999 V2000
   11.1540  -15.1286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9790  -15.1286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3914  -14.4141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2164  -14.4141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6289  -13.6995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4538  -13.6995    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.8662  -12.9856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6912  -12.9856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1037  -12.2711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9287  -12.2711    0.0000 N   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  2  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
M  END
> <DATABASE_ID>
NP0339119

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCC\C=N\CCCN

> <INCHI_IDENTIFIER>
InChI=1S/C7H17N3/c8-4-1-2-6-10-7-3-5-9/h6H,1-5,7-9H2/b10-6+

> <INCHI_KEY>
YAVLYBVKPXLZEQ-UXBLZVDNSA-N

> <FORMULA>
C7H17N3

> <MOLECULAR_WEIGHT>
143.23

> <EXACT_MASS>
143.142247559

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
17.89585800700923

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(E)-(4-aminobutylidene)(3-aminopropyl)amine

> <ALOGPS_LOGP>
-0.07

> <JCHEM_LOGP>
-1.2811043586666666

> <ALOGPS_LOGS>
-1.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA_STRONGEST_BASIC>
10.366991077088812

> <JCHEM_POLAR_SURFACE_AREA>
64.39999999999999

> <JCHEM_REFRACTIVITY>
44.301399999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dehydrospermidine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0339119 (Dehydrospermidine)
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PDB for NP0339119 (Dehydrospermidine)
HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  N   UNK     0      20.821 -28.240   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      22.361 -28.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      23.131 -26.906   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      24.671 -26.906   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      25.441 -25.572   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      26.980 -25.572   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      27.750 -24.240   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.290 -24.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.060 -22.906   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      31.600 -22.906   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0339119 (Dehydrospermidine)
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SMILES for NP0339119 (Dehydrospermidine)
NCCC\C=N\CCCN
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INCHI for NP0339119 (Dehydrospermidine)
InChI=1S/C7H17N3/c8-4-1-2-6-10-7-3-5-9/h6H,1-5,7-9H2/b10-6+
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Synonyms
ValueSource
N,C-Di(3-aminopropyl)-imineHMDB
N-(4-Aminobutylidene)-N-(3-aminopropyl)amineHMDB
DehydrospermidineChEBI
Chemical FormulaC7H17N3
Average Mass143.2300 Da
Monoisotopic Mass143.14225 Da
IUPAC Name(E)-(4-aminobutylidene)(3-aminopropyl)amine
Traditional Namedehydrospermidine
CAS Registry NumberNot Available
SMILES
NCCC\C=N\CCCN
InChI Identifier
InChI=1S/C7H17N3/c8-4-1-2-6-10-7-3-5-9/h6H,1-5,7-9H2/b10-6+
InChI KeyYAVLYBVKPXLZEQ-UXBLZVDNSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as shiff bases. These are aldimines where the nitrogen atom of the aldimine group is linked to an alkyl or aryl group.
KingdomOrganic compounds  
Super ClassOrganic nitrogen compounds  
ClassOrganonitrogen compounds  
Sub ClassImines  
Direct ParentShiff bases  
Alternative Parents
Substituents
  • Shiff base
    • 

  • Organic 1,3-dipolar compound
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Primary aliphatic amine
    • 

  • Amine
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.07ALOGPS
logP-1.3ChemAxon
logS-1.9ALOGPS
pKa (Strongest Basic)10.37ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area64.4 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity44.3 m³·mol⁻¹ChemAxon
Polarizability17.9 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0012925  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029209  
KNApSAcK IDNot Available
Chemspider ID21865491  
KEGG Compound IDC15853  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID48007  
Good Scents IDNot Available
References
General ReferencesNot Available