Record Information
Version2.0
Creation Date2012-05-31 13:52:33 -0600
Update Date2015-09-13 12:56:11 -0600
Secondary Accession Numbers
  • ECMDB01432
Identification
Name:Agmatine
DescriptionAgmatine (also known as (4-aminobutyl)guanidine) is the decarboxylation product of the amino acid arginine and is an intermediate in polyamine biosynthesis. (Wikipedia) In E. coli arginine metabolism, agmatine is produced from arginine in a reaction catalyzed by arginine decarboxylase (4.1.1.19). Another enzyme, agmatinase (EC 3.5.3.11), can then convert agmatine to putrescine, which is a polyamine that can be further converted to other products such as spermidine. (KEGG)
Structure
Thumb
Synonyms:
  • (4-aminobutyl)-Guanidine
  • (4-Aminobutyl)guanidine
  • 1-(4-Aminobutyl)guanidine
  • 1-Amino-4-guanidinobutane
  • 1-Amino-4-guanidobutane
  • 4-Guanidino-1-butanamine
  • Agmatine
  • Argmatine
  • N-(4-Aminobutyl)guanidine
  • N-(Aminoiminomethyl)-1,4-Butanediamine
  • N-4-Aminobutylguanidine
Chemical Formula:C5H14N4
Weight:Average: 130.1915
Monoisotopic: 130.121846468
InChI Key:QYPPJABKJHAVHS-UHFFFAOYSA-N
InChI:InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
CAS number:306-60-5
IUPAC Name:N-(4-aminobutyl)guanidine
Traditional IUPAC Name:agmatine
SMILES:NCCCCNC(N)=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
  • Carboximidamide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Imine
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
arginine metabolismPW000790 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • arginine degradation III (arginine decarboxylase/agmatinase pathway) PWY0-823
  • arginine dependent acid resistance PWY0-1299
  • putrescine biosynthesis I PWY-40
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
10± 0 uMK12 HB101199 Medium with Earle’s salts –which contains 21 amino acids, 17 vitamins, 10 components of nucleic acids, sodium acetate, glucose, NaC1, KCl, CaC12, MgS04, Na2HP04, and Fe(N03)3Mid Log PhaseShake flask37 oCPMID: 8742354
110± 0 uMK12 HB101199 Medium with Earle’s salts –which contains 21 amino acids, 17 vitamins, 10 components of nucleic acids, sodium acetate, glucose, NaC1, KCl, CaC12, MgS04, Na2HP04, and Fe(N03)3Stationary PhaseShake flask37 oCPMID: 8742354
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0002-0900000000-a9f6a71ff1ddda580ea9View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-00di-1910000000-4c97cf5e84d752009d1aView in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-00di-1910000000-de398de0f062b85c083cView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00di-1910000000-de398de0f062b85c083cView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00di-1910000000-de398de0f062b85c083cView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-008c-9000000000-ba695487db67f42d2617View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00e9-9700000000-dcb266f2466b6490a487View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-9000000000-e4747ffbbb1c0aa02f4eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00di-9000000000-e97e998997ab8bfcedb5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-001i-0900000000-4843789c1dd06e41493dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-00di-9200000000-a6b84c1241179a3739f8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-00di-9000000000-57f390519e8ddbcb80a8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-00di-9000000000-e38858b8c1a4fb2a6b14View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-00di-9000000000-2e6fd942608b84941a7dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-0900000000-075bad34dbbb7544e053View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-00di-9600000000-368edccb095766335b38View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-0900000000-6599222abf093d406584View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-0900000000-4843789c1dd06e41493dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9200000000-a6b84c1241179a3739f8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9000000000-57f390519e8ddbcb80a8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9000000000-e38858b8c1a4fb2a6b14View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9000000000-2e6fd942608b84941a7dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-0900000000-075bad34dbbb7544e053View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00di-9600000000-368edccb095766335b38View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-0229-9500000000-1c515d08e5bc52668dc4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03e9-3900000000-21dc8634e0e5c79fc825View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9300000000-55aa9e9ef7923b67457fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dl-9000000000-ec5b24cf1199482a883dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-9500000000-f8e119f2ba53222591a1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-9000000000-c4883e27e32ef6874c13View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-2b9c32eb2684272e86a2View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Atlas D: Molecular and physiological properties of clonidine-displacing substance. Ann N Y Acad Sci. 1995 Jul 12;763:314-24. Pubmed: 7677341
  • 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
  • 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
  • Hamana, K. (1996). "Distribution of diaminopropane and acetylspermidine in Enterobacteriaceae." Can J Microbiol 42:107-114. Pubmed: 8742354
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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 Mar 3. doi: 10.1038/nbt.2488. Pubmed: 23455439
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID17431
HMDB IDHMDB01432
Pubchem Compound ID199
Kegg IDC00179
ChemSpider ID194
WikipediaAgmatine
BioCyc IDAGMATHINE
EcoCyc IDAGMATHINE
Ligand ExpoAG2

Enzymes

General function:
Involved in catalytic activity
Specific function:
Catalyzes the biosynthesis of agmatine from arginine
Gene Name:
speA
Uniprot ID:
P21170
Molecular weight:
73898
Reactions
L-arginine = agmatine + CO(2).
General function:
Involved in carboxy-lyase activity
Specific function:
ADC can be found in two forms:biodegradative and biosynthetic. The biodegradative form may play a role in regulating pH by consuming proteins
Gene Name:
adiA
Uniprot ID:
P28629
Molecular weight:
84425
Reactions
L-arginine = agmatine + CO(2).
General function:
Involved in agmatinase activity
Specific function:
Catalyzes the formation of putrescine from agmatine
Gene Name:
speB
Uniprot ID:
P60651
Molecular weight:
33557
Reactions
Agmatine + H(2)O = putrescine + urea.

Transporters

General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in amino acid transmembrane transporter activity
Specific function:
Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach. Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons
Gene Name:
adiC
Uniprot ID:
P60061
Molecular weight:
46842
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368