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Showing metabocard for Homoagmatine (HMDB0031505)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:43:43 UTC
Update Date2023-02-21 17:20:41 UTC
HMDB IDHMDB0031505
Secondary Accession Numbers
  • HMDB31505
Metabolite Identification
Common NameHomoagmatine
DescriptionHomoagmatine belongs to the class of organic compounds known as guanidines. Guanidines are compounds containing a guanidine moiety, with the general structure (R1R2N)(R3R4N)C=N-R5. Based on a literature review very few articles have been published on Homoagmatine.
Structure
Data?1677000041
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031505 (Homoagmatine)

  Mrv0541 05061305582D          

 10  9  0  0  0  0            999 V2000
   -1.4586   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7441   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0296   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6020   -1.7309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1138   -1.7309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.9684    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -1.7309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  6  2  0  0  0  0
  9  6  1  0  0  0  0
 10  5  1  0  0  0  0
 10  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031505 (Homoagmatine)

HMDB0031505
     RDKit          3D
Homoagmatine
 26 25  0  0  0  0  0  0  0  0999 V2000
   -2.7479   -0.6619    0.8646 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7492    0.3983    0.1509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9337    1.0621   -0.2195 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4664    0.8999   -0.2705 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7417    0.2748   -1.3599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2472   -1.1117   -0.9739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6724   -0.9923    0.2198 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8617   -0.1171   -0.0416 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6765   -0.1077    1.2588 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8580    0.7283    1.1027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6445   -1.0909    1.2127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0117    2.1173   -0.1970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8002    0.5623   -0.5362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1076    1.7227    0.2554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4901    0.1260   -2.1728 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0914    0.9061   -1.6969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1175   -1.7232   -0.6546 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2237   -1.6108   -1.8188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0585   -2.0080    0.4601 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1388   -0.6044    1.0913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4671   -0.3953   -0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4803    0.9280   -0.2190 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0407    0.1904    2.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0555   -1.1261    1.4794 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7174    1.4718    0.3864 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7155    0.1614    0.9390 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
  9 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
M  END
Download

3D SDF for HMDB0031505 (Homoagmatine)

  Mrv0541 05061305582D          

 10  9  0  0  0  0            999 V2000
   -1.4586   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7441   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0296   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6020   -1.7309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1138   -1.7309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.9684    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -1.7309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  6  2  0  0  0  0
  9  6  1  0  0  0  0
 10  5  1  0  0  0  0
 10  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031505

> <DATABASE_NAME>
hmdb

> <SMILES>
NCCCCCNC(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C6H16N4/c7-4-2-1-3-5-10-6(8)9/h1-5,7H2,(H4,8,9,10)

> <INCHI_KEY>
XJHFHPPZQVRVHD-UHFFFAOYSA-N

> <FORMULA>
C6H16N4

> <MOLECULAR_WEIGHT>
144.218

> <EXACT_MASS>
144.137496532

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
17.200845517271382

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-(5-aminopentyl)guanidine

> <ALOGPS_LOGP>
-0.63

> <JCHEM_LOGP>
-0.734322349666667

> <ALOGPS_LOGS>
-1.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
12.517355286746653

> <JCHEM_POLAR_SURFACE_AREA>
87.92

> <JCHEM_REFRACTIVITY>
52.694199999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.28e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(5-aminopentyl)guanidine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0031505 (Homoagmatine)

HMDB0031505
     RDKit          3D
Homoagmatine
 26 25  0  0  0  0  0  0  0  0999 V2000
   -2.7479   -0.6619    0.8646 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7492    0.3983    0.1509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9337    1.0621   -0.2195 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4664    0.8999   -0.2705 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7417    0.2748   -1.3599 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2472   -1.1117   -0.9739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6724   -0.9923    0.2198 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8617   -0.1171   -0.0416 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6765   -0.1077    1.2588 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8580    0.7283    1.1027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6445   -1.0909    1.2127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0117    2.1173   -0.1970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8002    0.5623   -0.5362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1076    1.7227    0.2554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4901    0.1260   -2.1728 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0914    0.9061   -1.6969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1175   -1.7232   -0.6546 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2237   -1.6108   -1.8188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0585   -2.0080    0.4601 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1388   -0.6044    1.0913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4671   -0.3953   -0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4803    0.9280   -0.2190 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0407    0.1904    2.1001 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0555   -1.1261    1.4794 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7174    1.4718    0.3864 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7155    0.1614    0.9390 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
  9 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
M  END
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PDB for HMDB0031505 (Homoagmatine)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -2.723  -4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.056  -3.231   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.389  -3.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.055  -4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.612  -4.001   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -6.724  -3.231   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       3.946  -3.231   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       2.612  -5.541   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       1.278  -3.231   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    7                                                       
CONECT    5    3   10                                                       
CONECT    6    8    9   10                                                  
CONECT    7    4                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    5    6                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0031505 (Homoagmatine)

COMPND    HMDB0031505
HETATM    1  N1  UNL     1      -2.748  -0.662   0.865  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.749   0.398   0.151  1.00  0.00           C  
HETATM    3  N2  UNL     1      -3.934   1.062  -0.220  1.00  0.00           N  
HETATM    4  N3  UNL     1      -1.466   0.900  -0.271  1.00  0.00           N  
HETATM    5  C2  UNL     1      -0.742   0.275  -1.360  1.00  0.00           C  
HETATM    6  C3  UNL     1      -0.247  -1.112  -0.974  1.00  0.00           C  
HETATM    7  C4  UNL     1       0.672  -0.992   0.220  1.00  0.00           C  
HETATM    8  C5  UNL     1       1.862  -0.117  -0.042  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.676  -0.108   1.259  1.00  0.00           C  
HETATM   10  N4  UNL     1       3.858   0.728   1.103  1.00  0.00           N  
HETATM   11  H1  UNL     1      -3.644  -1.091   1.213  1.00  0.00           H  
HETATM   12  H2  UNL     1      -4.012   2.117  -0.197  1.00  0.00           H  
HETATM   13  H3  UNL     1      -4.800   0.562  -0.536  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.108   1.723   0.255  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.490   0.126  -2.173  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.091   0.906  -1.697  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.118  -1.723  -0.655  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.224  -1.611  -1.819  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.059  -2.008   0.460  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.139  -0.604   1.091  1.00  0.00           H  
HETATM   21  H11 UNL     1       2.467  -0.395  -0.905  1.00  0.00           H  
HETATM   22  H12 UNL     1       1.480   0.928  -0.219  1.00  0.00           H  
HETATM   23  H13 UNL     1       2.041   0.190   2.100  1.00  0.00           H  
HETATM   24  H14 UNL     1       3.055  -1.126   1.479  1.00  0.00           H  
HETATM   25  H15 UNL     1       3.717   1.472   0.386  1.00  0.00           H  
HETATM   26  H16 UNL     1       4.715   0.161   0.939  1.00  0.00           H  
CONECT    1    2    2   11
CONECT    2    3    4
CONECT    3   12   13
CONECT    4    5   14
CONECT    5    6   15   16
CONECT    6    7   17   18
CONECT    7    8   19   20
CONECT    8    9   21   22
CONECT    9   10   23   24
CONECT   10   25   26
END
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SMILES for HMDB0031505 (Homoagmatine)

NCCCCCNC(N)=N
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INCHI for HMDB0031505 (Homoagmatine)

InChI=1S/C6H16N4/c7-4-2-1-3-5-10-6(8)9/h1-5,7H2,(H4,8,9,10)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-Amino-5-guanidinopentaneHMDB
Chemical FormulaC6H16N4
Average Molecular Weight144.218
Monoisotopic Molecular Weight144.137496532
IUPAC Name1-(5-aminopentyl)guanidine
Traditional Name1-(5-aminopentyl)guanidine
CAS Registry Number18431-52-2
SMILES
NCCCCCNC(N)=N
InChI Identifier
InChI=1S/C6H16N4/c7-4-2-1-3-5-10-6(8)9/h1-5,7H2,(H4,8,9,10)
InChI KeyXJHFHPPZQVRVHD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as guanidines. Guanidines are compounds containing a guanidine moiety, with the general structure (R1R2N)(R3R4N)C=N-R5.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassGuanidines
Direct ParentGuanidines
Alternative Parents
Substituents
  • Guanidine
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008096
KNApSAcK IDC00055146
Chemspider ID14749615
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound21298950
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .