Showing metabocard for N1-Aminopropylagmatine (MMDBc0004803)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-05-14 22:38:28 UTC
Update Date2025-10-07 16:04:56 UTC
Metabolite IDMMDBc0004803
Metabolite Identification
Common NameN1-Aminopropylagmatine
DescriptionN1-Aminopropylagmatine is a polyamine metabolite described in biomedical literature. It serves as a key intermediate in the biosynthesis of unique polyamines, particularly in extreme thermophiles such as Thermus thermophilus. This compound is primarily produced from agmatine through the action of the enzyme coded by the speE gene (PMID:15983049 ). In certain bacterial strains, such as those with disrupted TK0882 genes, N1-aminopropylagmatine accumulates alongside agmatine in the cytoplasm, indicating its metabolic significance (PMID:20675472 ). The enzyme TK0882 has been shown to have a 43-fold-higher kcat/Km value for N1-aminopropylagmatine compared to agmatine, suggesting its primary role as a ureohydrolase in the production of spermidine (PMID:20675472 ). Additionally, the enzyme TK0147 functions as an aminopropyl transferase, favoring the conversion of agmatine to N1-aminopropylagmatine (PMID:20675472 ). In the context of polyamine biosynthesis, N1-aminopropylagmatine is crucial for the production of spermidine, highlighting its importance in the metabolic pathways of thermophilic organisms (PMID:15983049 ).
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fb4d2aaf508>


  Mrv0541 05031423482D          

 13 12  0  0  0  0            999 V2000
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  9  4  1  0  0  0  0
 10  8  2  0  0  0  0
 11  8  1  0  0  0  0
 12  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 13  8  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fb4d2aaf508>

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3D SDF for #<Metabolite:0x00007fb4d2aaf508>

  Mrv0541 05031423482D          

 13 12  0  0  0  0            999 V2000
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  9  4  1  0  0  0  0
 10  8  2  0  0  0  0
 11  8  1  0  0  0  0
 12  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 13  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0004803

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCNCCCCNC(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C8H21N5/c9-4-3-6-12-5-1-2-7-13-8(10)11/h12H,1-7,9H2,(H4,10,11,13)

> <INCHI_KEY>
XYCUJKFFVBCJEF-UHFFFAOYSA-N

> <FORMULA>
C8H21N5

> <MOLECULAR_WEIGHT>
187.2858

> <EXACT_MASS>
187.179695697

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
22.955832927034354

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-{4-[(3-aminopropyl)amino]butyl}guanidine

> <ALOGPS_LOGP>
-1.06

> <JCHEM_LOGP>
-1.4833346906666667

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA_STRONGEST_BASIC>
12.25445311428014

> <JCHEM_POLAR_SURFACE_AREA>
99.95

> <JCHEM_REFRACTIVITY>
65.68299999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.04e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-{4-[(3-aminopropyl)amino]butyl}guanidine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007fb4d2aaf508>
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PDB for #<Metabolite:0x00007fb4d2aaf508>
HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    7                                                       
CONECT    3    4    6                                                       
CONECT    4    3    9                                                       
CONECT    5    1   12                                                       
CONECT    6    3   12                                                       
CONECT    7    2   13                                                       
CONECT    8   10   11   13                                                  
CONECT    9    4                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12    5    6                                                       
CONECT   13    7    8                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for #<Metabolite:0x00007fb4d2aaf508>
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SMILES for #<Metabolite:0x00007fb4d2aaf508>
NCCCNCCCCNC(N)=N
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INCHI for #<Metabolite:0x00007fb4d2aaf508>
InChI=1S/C8H21N5/c9-4-3-6-12-5-1-2-7-13-8(10)11/h12H,1-7,9H2,(H4,10,11,13)
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Synonyms
ValueSource
N(1)-(3-Aminoaminopropyl)agmatineChEBI
N1-AminopropylagmatineKegg
Molecular FormulaC8H21N5
Average Mass187.2858
Monoisotopic Mass187.179695697
IUPAC Name1-{4-[(3-aminopropyl)amino]butyl}guanidine
Traditional Name1-{4-[(3-aminopropyl)amino]butyl}guanidine
CAS Registry NumberNot Available
SMILES
NCCCNCCCCNC(N)=N
InChI Identifier
InChI=1S/C8H21N5/c9-4-3-6-12-5-1-2-7-13-8(10)11/h12H,1-7,9H2,(H4,10,11,13)
InChI KeyXYCUJKFFVBCJEF-UHFFFAOYSA-N