NP-MRD: Showing NP-Card for (4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine (NP0183689)

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Record Information

Version

2.0

Created at

2022-09-03 22:38:33 UTC

Updated at

2022-09-03 22:38:33 UTC

NP-MRD ID

NP0183689

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine

Description

Homocaldopentamine belongs to the class of organic compounds known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen. (4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine was first documented in 2004 (PMID: 15747232). Based on a literature review a small amount of articles have been published on Homocaldopentamine (PMID: 19659728) (PMID: 23700086) (PMID: 29931720).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 51 50  0  0  0  0  0  0  0  0999 V2000
   -4.7731   -1.5878    0.8142 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9540   -1.6628    0.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9994   -0.7785   -1.1745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9221    0.6843   -0.9309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7073    1.1790   -0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5041    0.8461   -0.9624 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3126    1.2700   -0.2548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0750    0.4738    0.9983 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8453    0.9968    1.6952 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3446    0.9313    0.9222 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8641   -0.3653    0.6496 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1572   -0.1363   -0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0346    0.6989    0.7477 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2635    1.0045    0.1065 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0759   -0.1555   -0.0713 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3615    0.2994   -0.7344 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2337   -0.9197   -0.9397 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4919   -1.4987    0.3605 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1093   -2.3930    0.6729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9228   -1.3785    1.8132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9909   -2.7230   -0.3837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8463   -1.5820    0.6704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2647   -1.1534   -1.9153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0168   -0.9515   -1.6500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8417    1.0165   -0.4002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9804    1.1745   -1.9458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8138    2.3089   -0.1902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7024    0.7608    0.7934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5081    1.3675   -1.8676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3584    2.3556   -0.0847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4562    1.0799   -0.9456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8433   -0.5972    0.7263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9244    0.4204    1.6741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0180    2.0887    1.9216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7650    0.4261    2.6554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2827    1.5443    0.1045 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2183   -0.9967    0.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1843   -0.8568    1.5912 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5982   -1.1067   -0.4352 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9027    0.4635   -1.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1986    0.1875    1.7230 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4318    1.6366    0.9438 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1121    1.4625   -0.8106 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3522   -0.5979    0.9161 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5884   -0.9159   -0.7174 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1632    0.8196   -1.6725 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9040    0.9984   -0.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6789   -1.6225   -1.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1894   -0.6535   -1.4016 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3436   -2.5321    0.4005 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4796   -1.3305    0.6613 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  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
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  3 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  7 30  1  0
  7 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
  9 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 12 39  1  0
 12 40  1  0
 13 41  1  0
 13 42  1  0
 14 43  1  0
 15 44  1  0
 15 45  1  0
 16 46  1  0
 16 47  1  0
 17 48  1  0
 17 49  1  0
 18 50  1  0
 18 51  1  0
M  END


  Mrv1652309042200382D          

 18 17  0  0  0  0            999 V2000
    7.2336    5.0013    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9480    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6625    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3770    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0914    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8059    5.4138    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.5204    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2349    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9493    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6638    5.4138    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.3783    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0927    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8072    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5217    5.4138    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.2362    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9506    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6651    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3796    5.4138    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  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  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0183689

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCCNCCCNCCCNCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C13H33N5/c14-6-1-2-8-16-10-4-12-18-13-5-11-17-9-3-7-15/h16-18H,1-15H2

> <INCHI_KEY>
FPTWYQKWFMIJPT-UHFFFAOYSA-N

> <FORMULA>
C13H33N5

> <MOLECULAR_WEIGHT>
259.442

> <EXACT_MASS>
259.273596083

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
33.64535020801182

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine

> <JCHEM_LOGP>
-1.7584512920000006

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA_STRONGEST_BASIC>
10.8348920584406

> <JCHEM_POLAR_SURFACE_AREA>
88.13

> <JCHEM_REFRACTIVITY>
80.14799999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  N   UNK     0      13.503   9.336   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      14.836  10.106   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.170   9.336   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.504  10.106   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.837   9.336   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      20.171  10.106   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      21.505   9.336   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.838  10.106   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      24.172   9.336   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      25.506  10.106   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      26.839   9.336   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      28.173  10.106   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      29.507   9.336   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      30.840  10.106   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      32.174   9.336   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      33.508  10.106   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.842   9.336   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      36.175  10.106   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   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

View in JSmol

Synonyms

Value	Source
1,6-Diamino-4,8,12-triazahexadecane	MeSH

Chemical Formula

C₁₃H₃₃N₅

Average Mass

259.4420 Da

Monoisotopic Mass

259.27360 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

NCCCCNCCCNCCCNCCCN

InChI Identifier

InChI=1S/C13H33N5/c14-6-1-2-8-16-10-4-12-18-13-5-11-17-9-3-7-15/h16-18H,1-15H2

InChI Key

FPTWYQKWFMIJPT-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

Dialkylamines

Alternative Parents

Substituents

Secondary aliphatic amine
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary aliphatic amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	-1.8	ChemAxon
pKa (Strongest Basic)	10.83	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

170297

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

196565

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Nishibori N, Niitsu M, Fujihara S, Sagara T, Nishio S, Imai I: Occurrence of the polyamines caldopentamine and homocaldopentamine in axenic cultures of the red tide flagellates Chattonella antiqua and Heterosigma akashiwo (Raphidophyceae). FEMS Microbiol Lett. 2009 Sep;298(1):74-8. doi: 10.1111/j.1574-6968.2009.01701.x. Epub 2009 Jun 22. [PubMed:19659728 ]
Sagor GH, Liu T, Takahashi H, Niitsu M, Berberich T, Kusano T: Longer uncommon polyamines have a stronger defense gene-induction activity and a higher suppressing activity of Cucumber mosaic virus multiplication compared to that of spermine in Arabidopsis thaliana. Plant Cell Rep. 2013 Sep;32(9):1477-88. doi: 10.1007/s00299-013-1459-5. Epub 2013 May 23. [PubMed:23700086 ]
Nishio T, Yoshikawa Y, Fukuda W, Umezawa N, Higuchi T, Fujiwara S, Imanaka T, Yoshikawa K: Branched-Chain Polyamine Found in Hyperthermophiles Induces Unique Temperature-Dependent Structural Changes in Genome-Size DNA. Chemphyschem. 2018 Sep 18;19(18):2299-2304. doi: 10.1002/cphc.201800396. Epub 2018 Jul 10. [PubMed:29931720 ]
Hosoya R, Hamana K, Niitsu M, Itoh T: Polyamine analysis for chemotaxonomy of thermophilic eubacteria: Polyamine distribution profiles within the orders Aquificales, Thermotogales, Thermodesulfobacteriales, Thermales, Thermoanaerobacteriales, Clostridiales and Bacillales. J Gen Appl Microbiol. 2004 Oct;50(5):271-87. doi: 10.2323/jgam.50.271. [PubMed:15747232 ]
LOTUS database [Link]

Showing NP-Card for (4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine (NP0183689)

MOL for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

3D MOL for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

3D SDF for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

3D-SDF for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

PDB for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

3D PDB for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

SMILES for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

INCHI for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

Structure for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)

3D Structure for NP0183689 ((4-aminobutyl)[3-({3-[(3-aminopropyl)amino]propyl}amino)propyl]amine)