Putrescine (YMDB00132)

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Identification

YMDB ID

YMDB00132

Name

Putrescine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Putrescine, also known as 1,4-butanediamine or 1,4-diaminobutane, belongs to the class of organic compounds known as monoalkylamines. These are organic compounds containing an primary aliphatic amine group. Putrescine is a very strong basic compound (based on its pKa). Putrescine exists in all living species, ranging from bacteria to humans. Putrescine is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

1,4-Butanediamine
1,4-Butylenediamine
1,4-Diaminobutane
1,4-Tetramethylenediamine
Butylenediamine
Putrescin
Tetramethyldiamine
Tetramethylenediamine
Butane-1,4-diamine
H2N(CH2)4nh2
Putrescina
Putreszin
Tetramethylendiamin
1,4-Butanediammonium
1,4 Diaminobutane
1,4 Butanediamine

CAS number

110-60-1

Weight

Average: 88.1515
Monoisotopic: 88.100048394

InChI Key

KIDHWZJUCRJVML-UHFFFAOYSA-N

InChI

InChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2

IUPAC Name

butane-1,4-diamine

Traditional IUPAC Name

putrescine

Chemical Formula

C₄H₁₂N₂

SMILES

[H]N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as monoalkylamines. These are organic compounds containing an primary aliphatic amine group.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

Monoalkylamines

Alternative Parents

Substituents

Organopnictogen compound
Hydrocarbon derivative
Primary aliphatic amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

alkane-alpha,omega-diamine (CHEBI:17148 )
Biogenic amines (C00134 )
an aliphatic α,ω-diamine (PUTRESCINE )

Physical Properties

State

Solid

Charge

Melting point

27.5 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	-0.70 [SANGSTER (1994)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	236 g/L	ALOGPS
logP	-0.98	ALOGPS
logP	-0.85	ChemAxon
logS	0.43	ALOGPS
pKa (Strongest Basic)	10.51	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	52.04 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	27.38 m³·mol⁻¹	ChemAxon
Polarizability	11.07 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 Properties

Cellular Locations

extracellular
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Glutathione metabolism	PW002395
beta-Alanine metabolism	PW002381

KEGG Pathways

Arginine and proline metabolism	ec00330
Glutathione metabolism	ec00480
beta-Alanine metabolism	ec00410

SMPDB Reactions

Ornithine + hydron → Carbon dioxide + Putrescine

Putrescine + S-Adenosylmethioninamine → hydron + 5'-Methylthioadenosine + Spermidine

KEGG Reactions

Ornithine + hydron → Putrescine + Carbon dioxide

Putrescine + S-Adenosylmethioninamine → Spermidine + hydron + 5'-Methylthioadenosine

Concentrations

Intracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
74 ± 4 µM	YEB media with 0.5 mM glucose	aerobic	Baker's yeast	Experimentally Determined Not Available
Conversion Details Here

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-00di-1910000000-5694141cafbe39951441	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-00di-1900000000-eeb4354250406805ebe6	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-00di-8910000000-af71049ab8358b0042ff	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-00di-8900000000-0ba23327cabd9b2815f5	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-00di-2900000000-234e1b62f4e830226779	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-00di-1900000000-e29f1004e27fcb9cfe7b	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-001i-9000000000-224d3a5d3fbe7e1c6bd4	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-001i-9000000000-5759f91b24f2e27cc466	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - CI-B (Non-derivatized)	splash10-00di-9000000000-226a78b715ff64ec7067	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-1910000000-5694141cafbe39951441	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-1900000000-eeb4354250406805ebe6	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-8910000000-af71049ab8358b0042ff	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-8900000000-0ba23327cabd9b2815f5	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-2900000000-234e1b62f4e830226779	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-1900000000-e29f1004e27fcb9cfe7b	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-8900000000-0ba23327cabd9b2815f5	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-2900000000-234e1b62f4e830226779	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-1900000000-e29f1004e27fcb9cfe7b	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-1900000000-6861f65288867dab7690	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-2900000000-7923303f8f970b8d2dd6	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-9000000000-4d1729dd236ab6f44cd9	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00di-9000000000-f718a117761c1c7ea80d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-47752c8c65e2d83e78fb	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00du-9000000000-3603b20551e892ad6c5e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI RMU-6L) , Positive	splash10-001i-9000000000-224d3a5d3fbe7e1c6bd4	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - EI-B (HITACHI RMU-6M) , Positive	splash10-001i-9000000000-5759f91b24f2e27cc466	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - CI-B (HITACHI M-80) , Positive	splash10-00di-9000000000-226a78b715ff64ec7067	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-00dr-9000000000-0b342438cba3ac71bccb	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-00di-9000000000-8add450cd915232f7353	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9000000000-7a496471bdf7e391fdc8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-84da87b521647b4f42ab	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-001l-9000000000-3ca1e2cd5a7e125ac52e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-000i-9000000000-830221d5ea74a91c32e1	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00dr-9000000000-0b342438cba3ac71bccb	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-9000000000-8add450cd915232f7353	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-9000000000-7a496471bdf7e391fdc8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-9000000000-84da87b521647b4f42ab	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-001l-9000000000-3ca1e2cd5a7e125ac52e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-9000000000-830221d5ea74a91c32e1	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-00dl-9000000000-81dccfb50af8f3631f9b	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0079-9000000000-896934367d7bc245c8b3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05g0-9000000000-96d51f0aa46b0ab332d0	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-de02b50a4b8a279875e4	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-9000000000-73c448854a91ad5a9644	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9000000000-c600a93b8d737a254884	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-059f-9000000000-ce7ae61a17ef7cb9b2c2	JSpectraViewer
MS	Mass Spectrum (Electron Ionization)	splash10-001i-9000000000-2b410aa72c9bb951a79d	JSpectraViewer \| MoNA
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Pirkov, I., Norbeck, J., Gustafsson, L., Albers, E. (2008). "A complete inventory of all enzymes in the eukaryotic methionine salvage pathway." FEBS J 275:4111-4120.18625006
Tomitori, H., Kashiwagi, K., Asakawa, T., Kakinuma, Y., Michael, A. J., Igarashi, K. (2001). "Multiple polyamine transport systems on the vacuolar membrane in yeast." Biochem J 353:681-688.11171066

Synthesis Reference:

Dudley, H. W.; Thorpe, W. V. Synthesis of N-methylputrescine and of putrescine. Biochemical Journal (1925), 19 845-9.

External Links:

Resource	Link
CHEBI ID	17148
HMDB ID	HMDB01414
Pubchem Compound ID	1045
Kegg ID	C00134
ChemSpider ID	13837702
FOODB ID	FDB001494
Wikipedia	Putrescine
BioCyc ID	PUTRESCINE

Enzymes

Protein Details

1. Polyamine oxidase FMS1

General function:: Amino acid transport and metabolism
Specific function:: Involved in the production of beta-alanine, a precursor of pantothenic acid. Multicopy suppressor of fenpropimorph resistance
Gene Name:: FMS1
Uniprot ID:: P50264
Molecular weight:: 57805.10156

Reactions

Spermine + O(2) + H(2)O → spermidine + 3-aminopropanal + H(2)O(2).
Spermidine + O(2) + H(2)O → putrescine + 3-aminopropanal + H(2)O(2).
N(1)-acetylspermine + O(2) + H(2)O → spermidine + 3-acetamidopropanal + H(2)O(2).
N(1)-acetylspermidine + O(2) + H(2)O → putrescine + 3-acetamidopropanal + H(2)O(2).
N(8)-acetylspermidine + O(2) + H(2)O → 4-acetamidobutanal + trimethylenediamine + H(2)O(2).

Protein Details

2. Spermidine synthase

General function:: Involved in catalytic activity
Specific function:: S-adenosylmethioninamine + putrescine = 5'-S- methyl-5'-thioadenosine + spermidine
Gene Name:: SPE3
Uniprot ID:: Q12074
Molecular weight:: 33323.80078

Reactions

S-adenosylmethioninamine + putrescine → 5'-S-methyl-5'-thioadenosine + spermidine.

Protein Details

3. Ornithine decarboxylase

General function:: Involved in catalytic activity
Specific function:: L-ornithine = putrescine + CO(2)
Gene Name:: SPE1
Uniprot ID:: P08432
Molecular weight:: 52284.80078

Reactions

L-ornithine → putrescine + CO(2).

Transporters

Protein Details

1. Polyamine transporter 4

General function:: Involved in transmembrane transport
Specific function:: Cell membrane polyamine/proton antiporter, involved in the detoxification of excess polyamines in the cytoplasm. Recognizes spermidine, spermine and the antimalarial drug quinidine, but not quinine, chloroquine and mefloquine
Gene Name:: TPO4
Uniprot ID:: Q12256
Molecular weight:: 73222.20313

Protein Details

2. Polyamine transporter TPO5

General function:: Involved in transport
Specific function:: Required for polyamine transport. Transports putrescine effectively and spermidine less effectively
Gene Name:: TPO5
Uniprot ID:: P36029
Molecular weight:: 69242.0

Protein Details

3. Polyamine transporter 1

General function:: Involved in transmembrane transport
Specific function:: Cell membrane polyamine/proton antiporter, involved in the detoxification of excess polyamines in the cytoplasm. Catalyzes polyamine uptake at alkaline pH and excretion at acidic pH. Recognizes spermidine, spermine and putrescine, the polyamine analogs methylglyoxal bis(guanylhydrazone) (MGBG) and paraquat, the antimalarial drug quinidine, and cycloheximide. Confers resistance to the non-steroidal anti-inflammatory drug indomethacin
Gene Name:: TPO1
Uniprot ID:: Q07824
Molecular weight:: 64271.60156

Structure for #<Compound:0xa73a2ddc>

Enzymes

Reactions

Reactions

Reactions

Transporters