Showing metabocard for Agmatine (MMDBc0000390)

Not Available
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:36:42 UTC
Update Date2024-10-09 22:27:50 UTC
Metabolite IDMMDBc0000390
Metabolite Identification
Common NameAgmatine
DescriptionAgmatine ((4-aminobutyl)guanidine, NH2-CH2-CH2-CH2-CH2-NH-C(-NH2)(=NH)) is the decarboxylation product of the amino acid arginine and is an intermediate in polyamine biosynthesis. It is a putative neurotransmitter. It is synthesized in the brain, stored in synaptic vesicles, accumulated by uptake, released by membrane depolarization, and inactivated by agmatinase. Agmatine binds to 2-adrenergic receptor and imidazoline binding sites, and blocks NMDA receptors and other cation ligand-gated channels. Agmatine inhibits nitric oxide synthase (NOS), and induces the release of some peptide hormones. Treatment with exogenous agmatine exerts neuroprotective effects in animal models of neurotrauma.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb4c0d2f80>


  Mrv1652305271900022D          

  9  8  0  0  0  0            999 V2000
    0.1594   -0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8730    0.3227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5541    0.3227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5904   -0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2715   -0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3040    0.3227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5904   -0.9186    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9852    0.3227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7025   -0.0912    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
  4  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fdb4c0d2f80>

HMDB0001432
     RDKit          3D
Agmatine
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.5687   -0.0701   -0.3507 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7188    0.7771    0.1741 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0066    2.1645    0.0574 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5515    0.3358    0.8362 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4892   -0.3378    0.1291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6463   -0.7085    1.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7491   -1.4069    0.3240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3697   -0.6081   -0.7723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9650    0.6126   -0.3978 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4054   -1.0958   -0.2932 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5846    2.8815    0.6961 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6559    2.5053   -0.6799 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4395    0.4919    1.8554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0694    0.3886   -0.6260 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8636   -1.1959   -0.4508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2366   -1.4163    1.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9750    0.2004    1.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2940   -2.3191   -0.1537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5111   -1.7991    1.0239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5851   -0.4004   -1.5444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1363   -1.2459   -1.2612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9221    0.8779    0.5948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9629    1.3681   -1.0758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  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
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
  9 23  1  0
M  END
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3D SDF for #<Metabolite:0x00007fdb4c0d2f80>


  Mrv1652305271900022D          

  9  8  0  0  0  0            999 V2000
    0.1594   -0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8730    0.3227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5541    0.3227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5904   -0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2715   -0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3040    0.3227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5904   -0.9186    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9852    0.3227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7025   -0.0912    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
  4  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000390

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCNC(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)

> <INCHI_KEY>
QYPPJABKJHAVHS-UHFFFAOYSA-N

> <FORMULA>
C5H14N4

> <MOLECULAR_WEIGHT>
130.1915

> <EXACT_MASS>
130.121846468

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.013803645262437

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-(4-aminobutyl)guanidine

> <ALOGPS_LOGP>
-1.01

> <JCHEM_LOGP>
-1.1788910146666667

> <ALOGPS_LOGS>
-1.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
12.605114263747222

> <JCHEM_POLAR_SURFACE_AREA>
87.92

> <JCHEM_REFRACTIVITY>
48.0932

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
agmatine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fdb4c0d2f80>

HMDB0001432
     RDKit          3D
Agmatine
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.5687   -0.0701   -0.3507 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7188    0.7771    0.1741 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0066    2.1645    0.0574 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5515    0.3358    0.8362 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4892   -0.3378    0.1291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6463   -0.7085    1.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7491   -1.4069    0.3240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3697   -0.6081   -0.7723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9650    0.6126   -0.3978 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4054   -1.0958   -0.2932 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5846    2.8815    0.6961 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6559    2.5053   -0.6799 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4395    0.4919    1.8554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0694    0.3886   -0.6260 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8636   -1.1959   -0.4508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2366   -1.4163    1.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9750    0.2004    1.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2940   -2.3191   -0.1537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5111   -1.7991    1.0239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5851   -0.4004   -1.5444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1363   -1.2459   -1.2612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9221    0.8779    0.5948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9629    1.3681   -1.0758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  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
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
  9 23  1  0
M  END
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PDB for #<Metabolite:0x00007fdb4c0d2f80>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       0.298  -0.170   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.630   0.602   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -1.034   0.602   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.969  -0.170   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.373  -0.170   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.301   0.602   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       2.969  -1.715   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -3.706   0.602   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -5.045  -0.170   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6    7                                                  
CONECT    5    3    8                                                       
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    5    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007fdb4c0d2f80>

COMPND    HMDB0001432
HETATM    1  N1  UNL     1       3.569  -0.070  -0.351  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.719   0.777   0.174  1.00  0.00           C  
HETATM    3  N2  UNL     1       3.007   2.165   0.057  1.00  0.00           N  
HETATM    4  N3  UNL     1       1.552   0.336   0.836  1.00  0.00           N  
HETATM    5  C2  UNL     1       0.489  -0.338   0.129  1.00  0.00           C  
HETATM    6  C3  UNL     1      -0.646  -0.708   1.054  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.749  -1.407   0.324  1.00  0.00           C  
HETATM    8  C5  UNL     1      -2.370  -0.608  -0.772  1.00  0.00           C  
HETATM    9  N4  UNL     1      -2.965   0.613  -0.398  1.00  0.00           N  
HETATM   10  H1  UNL     1       3.405  -1.096  -0.293  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.585   2.881   0.696  1.00  0.00           H  
HETATM   12  H3  UNL     1       3.656   2.505  -0.680  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.440   0.492   1.855  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.069   0.389  -0.626  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.864  -1.196  -0.451  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.237  -1.416   1.803  1.00  0.00           H  
HETATM   17  H8  UNL     1      -0.975   0.200   1.581  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.294  -2.319  -0.154  1.00  0.00           H  
HETATM   19  H10 UNL     1      -2.511  -1.799   1.024  1.00  0.00           H  
HETATM   20  H11 UNL     1      -1.585  -0.400  -1.544  1.00  0.00           H  
HETATM   21  H12 UNL     1      -3.136  -1.246  -1.261  1.00  0.00           H  
HETATM   22  H13 UNL     1      -2.922   0.878   0.595  1.00  0.00           H  
HETATM   23  H14 UNL     1      -2.963   1.368  -1.076  1.00  0.00           H  
CONECT    1    2    2   10
CONECT    2    3    4
CONECT    3   11   12
CONECT    4    5   13
CONECT    5    6   14   15
CONECT    6    7   16   17
CONECT    7    8   18   19
CONECT    8    9   20   21
CONECT    9   22   23
END
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SMILES for #<Metabolite:0x00007fdb4c0d2f80>

NCCCCNC(N)=N
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INCHI for #<Metabolite:0x00007fdb4c0d2f80>

InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
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Synonyms
ValueSource
(4-Aminobutyl) guanidineChEBI
(4-Aminobutyl)guanidineChEBI
N-(4-Aminobutyl)guanidineChEBI
(4-Aminobutyl)-guanidineHMDB
1-(4-Aminobutyl)guanidineHMDB
1-Amino-4-guanidinobutaneHMDB
1-Amino-4-guanidobutaneHMDB
4-Guanidino-1-butanamineHMDB
AgmatiniumHMDB
ArgmatineHMDB
N-(Aminoiminomethyl)-1,4-butanediamineHMDB
N-4-AminobutylguanidineHMDB
1 Amino 4 guanidinobutaneHMDB
4-(Aminobutyl)guanidineHMDB
Molecular FormulaC5H14N4
Average Mass130.1915
Monoisotopic Mass130.121846468
IUPAC NameN-(4-aminobutyl)guanidine
Traditional Nameagmatine
CAS Registry NumberNot Available
SMILES
NCCCCNC(N)=N
InChI Identifier
InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
InChI KeyQYPPJABKJHAVHS-UHFFFAOYSA-N