P. aeruginosa Metabolome Database: agmatine (PAMDB110682)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information
Version	1.0
Update Date	1/22/2018 11:54:54 AM
Metabolite ID	PAMDB110682
Identification
Name:	agmatine
Description:	The dication resulting from deprotonation of the amino and guanidino groups of agmatine; major species at pH 7.3.
Structure	🔍MOL SDF PDB SMILES InChI View Structure Structure for agmatine (PAMDB110682)
Synonyms:	RCH2NH2 RCH(2)NH(2)' WIDTH 200);" onmouseout="return nd();">an aliphatic amine

Chemical Formula: C₅H₁₆N₄ Average Molecular Weight: 132.21Monoisotopic Molecular Weight: 132.1374965344InChI Key: QYPPJABKJHAVHS-UHFFFAOYSA-PInChI: InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)/p+2CAS number: 306-60-5IUPAC Name:{amino[(4-azaniumylbutyl)amino]methylidene}azanium Traditional IUPAC Name: agmatineSMILES:C(CCC[N+])NC(=[N+])N Chemical Taxonomy Taxonomy DescriptionThis compound belongs to the class of chemical entities known as guanidines. These are compounds containing a guanidine moiety, with the general structure (R1R2N)(R3R4N)C=N-R5. Kingdom Chemical entities Super ClassOrganic compounds Class Organic nitrogen compounds Sub ClassOrganonitrogen compounds Direct Parent Guanidines Alternative Parents

Substituents

Guanidine
Carboximidamide
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary aliphatic amine
Imine
Amine
Aliphatic acyclic compound

Molecular Framework Aliphatic acyclic compoundsExternal Descriptors

guanidines (CHEBI:17431 )
primary amino compound (CHEBI:17431 )
Amines (C00179 )

Physical PropertiesState: SolidCharge:+2 Melting point: Not AvailableExperimental Properties:

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	3.61 mg/mL	ALOGPS
logP	-1	ALOGPS
logP	-1.2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Basic)	12.61	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	87.92 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	48.09 m³·mol^-1	ChemAxon
Polarizability	15.01 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological PropertiesCellular Locations: Not AvailableReactions:

Pathways:

superpathway of L-arginine, putrescine, and 4-aminobutyrate degradationARGDEG-PWY
superpathway of polyamine biosynthesis IPOLYAMSYN-PWY
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)PWY0-823
putrescine biosynthesis IPWY-40
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)ARGDEG-III-PWY
arginine degradation IIARGDEG-II-PWY
arginine dependent acid resistancePWY0-1299
putrescine biosynthesis IIPWY-43
superpathway of polyamine biosynthesis IIPOLYAMINSYN3-PWY

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)	splash10-0002-0900000000-a9f6a71ff1ddda580ea9	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)	splash10-00di-1910000000-4c97cf5e84d752009d1a	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-00di-1910000000-de398de0f062b85c083c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00e9-9700000000-dcb266f2466b6490a487	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-e4747ffbbb1c0aa02f4e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-e97e998997ab8bfcedb5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-001i-0900000000-4843789c1dd06e41493d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-00di-9200000000-a6b84c1241179a3739f8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9000000000-57f390519e8ddbcb80a8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-e38858b8c1a4fb2a6b14	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00di-9000000000-2e6fd942608b84941a7d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-001i-0900000000-075bad34dbbb7544e053	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-00di-9600000000-368edccb095766335b38	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03e9-3900000000-21dc8634e0e5c79fc825	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9300000000-55aa9e9ef7923b67457f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-9000000000-ec5b24cf1199482a883d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9500000000-f8e119f2ba53222591a1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9000000000-c4883e27e32ef6874c13	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-2b9c32eb2684272e86a2	View in MoNA
1D NMR	1H NMR Spectrum	Not Available
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available

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. [15028565 ]
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. [9174263 ]
Atlas D: Molecular and physiological properties of clonidine-displacing substance. Ann N Y Acad Sci. 1995 Jul 12;763:314-24. [7677341 ]
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. [16820162 ]
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. [23455439 ]

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Resource	Link
CAS	306-60-5
ChEBI	58145
ChemSpider	4422891
HMDB	HMDB01432
IAF1260	34153
KEGG	C00179
MetaboLights	MTBLC58145
PubChem	5257176

agmatine (PAMDB110682)

Structure for agmatine (PAMDB110682)