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Showing NP-Card for N1-Acetylspermidine (NP0086744)

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Record Information
Version2.0
Created at2022-05-11 16:29:47 UTC
Updated at2022-05-11 16:29:47 UTC
NP-MRD IDNP0086744
Secondary Accession NumbersNone
Natural Product Identification
Common NameN1-Acetylspermidine
DescriptionN1-Acetylspermidine belongs to the class of organic compounds known as carboximidic acids. These are organic acids with the general formula RC(=N)-OH (R=H, organic group). An acetylspermidine having the acetyl group at the N1-position. N1-Acetylspermidine is a very strong basic compound (based on its pKa). N1-Acetylspermidine exists in all living species, ranging from bacteria to humans. Outside of the human body, N1-Acetylspermidine has been detected, but not quantified in, several different foods, such as purple mangosteens, highbush blueberries, corianders, silver lindens, and komatsuna. N1-Acetylspermidine is found in Apis cerana and Trypanosoma brucei. N1-Acetylspermidine was first documented in 1978 (PMID: 708851). This could make N1-acetylspermidine a potential biomarker for the consumption of these foods (PMID: 6861156) (PMID: 6897929) (PMID: 7066912).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086744 (N1-Acetylspermidine)


  Mrv0541 02231219022D          

 13 12  0  0  0  0            999 V2000
    0.0569   -0.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9832    0.2126    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7706    0.2961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7007   -0.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4843   -0.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4144    0.2126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    0.3910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1318   -0.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5798   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8455    0.2126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2972    0.3910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5798   -0.8466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5592   -0.2012    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
 10 13  1  0  0  0  0
M  END
Download

3D MOL for NP0086744 (N1-Acetylspermidine)

     RDKit          3D

 34 33  0  0  0  0  0  0  0  0999 V2000
    5.8918    1.3180    0.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0404    0.2838   -0.4337 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5170   -0.4432   -1.3403 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6902    0.1228   -0.0187 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8145   -0.8692   -0.6088 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4558   -0.7409    0.0934 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4879   -1.7445   -0.4603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7988   -1.6551    0.1866 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4481   -0.4363   -0.1678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7938   -0.2682    0.5209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3417    1.0690    0.0397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6900    1.3548    0.6696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6258    0.3220    0.3139 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4666    0.9193    1.0587 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5792    1.7045   -0.5781 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2868    2.2010    0.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3192    0.7475    0.7466 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1664   -1.8966   -0.3767 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6584   -0.7363   -1.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0887    0.3043   -0.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6462   -0.9436    1.1559 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4115   -1.5626   -1.5639 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9407   -2.7616   -0.3464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3935   -2.4439   -0.1682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6889   -0.4351   -1.2720 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8909    0.4803    0.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5029   -1.0738    0.2723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6906   -0.2199    1.6166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4120    1.0962   -1.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6622    1.8983    0.3172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0627    2.3584    0.3870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5548    1.3748    1.7834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3467   -0.1125   -0.6002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5579    0.7883    0.1395 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
 13 34  1  0
M  END
Download

3D SDF for NP0086744 (N1-Acetylspermidine)


  Mrv0541 02231219022D          

 13 12  0  0  0  0            999 V2000
    0.0569   -0.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9832    0.2126    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7706    0.2961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7007   -0.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4843   -0.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4144    0.2126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    0.3910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1318   -0.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5798   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8455    0.2126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2972    0.3910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5798   -0.8466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5592   -0.2012    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
 10 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086744

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)NCCCNCCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C9H21N3O/c1-9(13)12-8-4-7-11-6-3-2-5-10/h11H,2-8,10H2,1H3,(H,12,13)

> <INCHI_KEY>
MQTAVJHICJWXBR-UHFFFAOYSA-N

> <FORMULA>
C9H21N3O

> <MOLECULAR_WEIGHT>
187.2825

> <EXACT_MASS>
187.168462309

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
23.110031458857055

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{3-[(4-aminobutyl)amino]propyl}acetamide

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-1.3307173369999998

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.528018704992306

> <JCHEM_PKA_STRONGEST_BASIC>
10.665494107139267

> <JCHEM_POLAR_SURFACE_AREA>
67.14999999999999

> <JCHEM_REFRACTIVITY>
54.412200000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.72e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N1-acetylspermidine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086744 (N1-Acetylspermidine)

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PDB for NP0086744 (N1-Acetylspermidine)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       0.106  -0.220   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.835   0.397   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       1.438   0.553   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.175  -0.376   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.771  -0.220   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.507   0.397   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       5.350   0.730   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -5.846  -0.376   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.682  -0.043   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -7.178   0.397   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.021   0.730   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.682  -1.580   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0      -8.511  -0.376   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11   12                                                  
CONECT   10    8   13                                                       
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for NP0086744 (N1-Acetylspermidine)
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SMILES for NP0086744 (N1-Acetylspermidine)
CC(=O)NCCCNCCCCN
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INCHI for NP0086744 (N1-Acetylspermidine)
InChI=1S/C9H21N3O/c1-9(13)12-8-4-7-11-6-3-2-5-10/h11H,2-8,10H2,1H3,(H,12,13)
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View in JSmol
Synonyms
ValueSource
1-N-AcetylspermidineChEBI
An N-acetylspermidineHMDB
N(1)-AcetylspermidineHMDB
N-(3-((4-Aminobutyl)amino)propyl)-acetamideHMDB
N-(3-((4-Aminobutyl)amino)propyl)acetamideHMDB
N-AcetylspermidineHMDB
N1-AcetylspermidineChEBI
Chemical FormulaC9H21N3O
Average Mass187.2825 Da
Monoisotopic Mass187.16846 Da
IUPAC NameN-{3-[(4-aminobutyl)amino]propyl}acetamide
Traditional NameN1-acetylspermidine
CAS Registry NumberNot Available
SMILES
CC(=O)NCCCNCCCCN
InChI Identifier
InChI=1S/C9H21N3O/c1-9(13)12-8-4-7-11-6-3-2-5-10/h11H,2-8,10H2,1H3,(H,12,13)
InChI KeyMQTAVJHICJWXBR-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Apis ceranaLOTUS Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carboximidic acids. These are organic acids with the general formula RC(=N)-OH (R=H, organic group).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboximidic acids and derivatives  
Sub ClassCarboximidic acids  
Direct ParentCarboximidic acids  
Alternative Parents
Substituents
  • Organic 1,3-dipolar compound
    • 

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

  • Secondary amine
    • 

  • Secondary aliphatic amine
    • 

  • Carboximidic acid
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • 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-0.47ALOGPS
logP-1.3ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)16.53ChemAxon
pKa (Strongest Basic)10.67ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area67.15 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity54.41 m³·mol⁻¹ChemAxon
Polarizability23.11 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001276  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022530  
KNApSAcK IDNot Available
Chemspider ID482  
KEGG Compound IDC00612  
BioCyc IDCPD-568  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID3323  
PubChem Compound496  
PDB IDNot Available
ChEBI ID17927  
Good Scents IDNot Available
References
General References
  1. Hrushesky WJ, Merdink J, Abdel-Monem MM: Circadian rhythmicity of polyamine urinary excretion. Cancer Res. 1983 Aug;43(8):3944-7. [PubMed:6861156  ] 
  2. Seiler N, Graham A, Bartholeyns J: Enhanced urinary excretion of N1-acetylspermidine and the presence of tumors. Cancer Res. 1981 Apr;41(4):1572-3. [PubMed:6897929  ] 
  3. Abdel-Monem MM, Merdink JL, Theologides A: Urinary excretion of monoacetyl polyamines in patients with non-Hodgkin's lymphoma. Cancer Res. 1982 May;42(5):2097-8. [PubMed:7066912  ] 
  4. Smith RG, Bartos D, Bartos F, Grettie DP, Frick W, Campbell RA, Daves GD Jr: 1-N-Acetylspermidine: occurrence in normal human serum. Biomed Mass Spectrom. 1978 Sep;5(9):515-7. doi: 10.1002/bms.1200050902. [PubMed:708851  ]