Np mrd loader

Showing NP-Card for Agmatine (NP0001333)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:59:02 UTC
NP-MRD IDNP0001333
Secondary Accession NumbersNone
Natural Product 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001333 (Agmatine)


  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
Download

3D MOL for NP0001333 (Agmatine)

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
Download

3D SDF for NP0001333 (Agmatine)


  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>
NP0001333

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0001333 (Agmatine)

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
Download

PDB for NP0001333 (Agmatine)

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
Download

3D PDB for NP0001333 (Agmatine)

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
Download

SMILES for NP0001333 (Agmatine)

NCCCCNC(N)=N
Download

INCHI for NP0001333 (Agmatine)

InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
Download
View in JSmol
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
Chemical FormulaC5H14N4
Average Mass130.1915 Da
Monoisotopic Mass130.12185 Da
IUPAC NameN-(4-aminobutyl)guanidine
Traditional Nameagmatine
CAS Registry Number306-60-5
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-08-10View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Canavalia gladiataLOTUS Database
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Glycine maxKNApSAcK Database
Hippospongia communisLOTUS Database
Homo sapiensLOTUS Database
Hordeum vulgareKNApSAcK Database
Lagopus mutaFooDB
Lathyrus sativusKNApSAcK Database
Lens culinarisFooDB
LeporidaeFooDB
Lepus timidusFooDB
Lyallia kerguelensisKNApSAcK Database
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Mizuhopecten yessoensisLOTUS Database
Mus musculusLOTUS Database
Nephila clavataLOTUS Database
Nicotiana tabacum (L.)KNApSAcK Database
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Psophocarpus tetragonolobusKNApSAcK Database
Raphanus sativus var. longipinnatusFooDB
Santalum albumKNApSAcK Database
Sesamum indicumKNApSAcK Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Vicia sativaKNApSAcK Database
Wisteria floribundaKNApSAcK Database
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
  • Carboximidamide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Imine
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point234.80 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility900200 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-1.550 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility3.61 g/LALOGPS
logP-1ALOGPS
logP-1.2ChemAxon
logS-1.6ALOGPS
pKa (Strongest Basic)12.61ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area87.92 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity48.09 m³·mol⁻¹ChemAxon
Polarizability15.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001432
DrugBank IDDB08838
Phenol Explorer Compound IDNot Available
FoodDB IDFDB008310
KNApSAcK IDC00001400
Chemspider ID194
KEGG Compound IDC00179
BioCyc IDAGMATHINE
BiGG ID34153
Wikipedia LinkAgmatine
METLIN ID3523
PubChem Compound199
PDB IDNot Available
ChEBI ID17431
Good Scents IDrw1628071
References
General References
  1. Halaris A, Piletz JE: Relevance of imidazoline receptors and agmatine to psychiatry: a decade of progress. Ann N Y Acad Sci. 2003 Dec;1009:1-20. [PubMed:15028565 ]
  2. Feng Y, Halaris AE, Piletz JE: Determination of agmatine in brain and plasma using high-performance liquid chromatography with fluorescence detection. J Chromatogr B Biomed Sci Appl. 1997 Apr 11;691(2):277-86. [PubMed:9174263 ]
  3. Atlas D: Molecular and physiological properties of clonidine-displacing substance. Ann N Y Acad Sci. 1995 Jul 12;763:314-24. [PubMed:7677341 ]
  4. Zhao S, Wang B, Yuan H, Xiao D: Determination of agmatine in biological samples by capillary electrophoresis with optical fiber light-emitting-diode-induced fluorescence detection. J Chromatogr A. 2006 Aug 4;1123(1):138-41. Epub 2006 Jul 3. [PubMed:16820162 ]
  5. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]