Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000075
Identification
Name: L-Lysine
Description:L-lysine is an alpha-amino acid with the chemical formula HO2CCH(NH2)(CH2)4NH2. Lysine is a basic amino acid as are arginine and histidine. Lysine is a proteogenic amino acid, meaning that it is used in protein synthesis. Lysine typically constitutes about 7-8% of an average protein. The epsilon-amino group often participates in hydrogen bonding and as a general base in catalysis. Common posttranslational modifications include methylation of the epsilon-amino group, giving methyl-, dimethyl-, and trimethyllysine. In bacteria, lysine is synthesized from aspartic acid, which is first converted to aspartyl-semialdehyde.
Structure
Thumb
Synonyms:
  • (+)-S-Lysine
  • (S)-2,6-diamino-Hexanoate
  • (S)-2,6-diamino-Hexanoic acid
  • (S)-2,6-Diaminohexanoate
  • (S)-2,6-Diaminohexanoic acid
  • (S)-a,e-Diaminocaproate
  • (S)-a,e-Diaminocaproic acid
  • (S)-Lysine
  • 2,6-Diaminohexanoate
  • 2,6-Diaminohexanoic acid
  • 6-Amino-Aminutrin
  • 6-Amino-L-Norleucine
  • A-Lysine
  • Alpha-Lysine
  • Aminutrin
  • H-Lys-oh
  • K
  • L-(+)-Lysine
  • L-2,6-Diainohexanoate
  • L-2,6-Diainohexanoic acid
  • L-2,6-Diaminocaproate
  • L-2,6-Diaminocaproic acid
  • L-Lys
  • Lys
  • Lysine
  • Lysine acid
  • α-Lysine
Chemical Formula: C6H14N2O2
Average Molecular Weight: 146.1876
Monoisotopic Molecular Weight: 146.105527702
InChI Key: KDXKERNSBIXSRK-YFKPBYRVSA-N
InChI:InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1
CAS number: 56-87-1
IUPAC Name:(2S)-2,6-diaminohexanoic acid
Traditional IUPAC Name: L-lysine
SMILES:NCCCC[C@H](N)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
Kingdom Organic compounds
Super ClassOrganic acids and derivatives
Class Carboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct Parent L-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Medium-chain fatty acid
  • Amino fatty acid
  • Fatty acyl
  • Fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:1
Melting point: 224.5 °C
Experimental Properties:
PropertyValueSource
Water Solubility:1000.0 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP:-3.05 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility105.0 mg/mLALOGPS
logP-3.8ALOGPS
logP-3.2ChemAxon
logS-0.14ALOGPS
pKa (Strongest Acidic)2.74ChemAxon
pKa (Strongest Basic)10.29ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.81 m3·mol-1ChemAxon
Polarizability15.84 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-00di-3910000000-98c565675de67aa87900View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0ab9-1910000000-87ef8534f592041f50f2View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0a4i-1921000000-84f7815b0f650fa17444View in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-001i-9600000000-823408dba509cb204acfView in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-00di-3910000000-4f5578af5e7d8b6c49f7View in MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0adi-1921000000-4e56d95e623e792f9e6bView in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-003r-8900000000-470a0beb4f338ed89bcaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-74e9193d9d33c2509bfaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a59-9000000000-822c4e78250fffa56e39View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0002-0900000000-04f9a62a77fb5a37ca22View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-9000000000-035035ecfa084671479bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-5bb15839f86f4fca0d0bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-6c8ef03aa83eb1cab35bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-01ot-0910000000-c182a7dcdbc260666978View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0a4j-0900000000-6c5f378cef2f14204e15View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-001i-0900000000-41e1a6499097748934b0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0390000000-7270a0b85b9e3f9f6373View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0002-0900000000-a997e809874357908880View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0002-2900000000-f64110414f82c93e1fe8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-014m-9200000000-33a38e6370811c5ddc82View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-3a8b0b6e62f5c66d3720View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-d5167570d11d77fd541eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-0002-0900000000-a46231bd529176101129View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-001i-9200000000-f8b9f01b2a9886c51df9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-001i-9000000000-ace0361476d939043e98View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-001i-9000000000-5b06b6e9dcf9faf8e89cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-053r-9000000000-2894ef6d7f72ea71688eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - CE-ESI-TOF (CE-system connected to 6210 Time-of-Flight MS, Agilent) , Positivesplash10-0002-0900000000-290902f43cf851e8ef5eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-9300000000-f81193f6b50235ec8147View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-9300000000-8931d2193adab166d5e4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0002-0900000000-b4825cc64fcb830c6967View in MoNA
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Cynober LA: Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition. 2002 Sep;18(9):761-6. Pubmed: 12297216
  • Engelborghs S, Marescau B, De Deyn PP: Amino acids and biogenic amines in cerebrospinal fluid of patients with Parkinson's disease. Neurochem Res. 2003 Aug;28(8):1145-50. Pubmed: 12834252
  • Faraasen S, Voros J, Csucs G, Textor M, Merkle HP, Walter E: Ligand-specific targeting of microspheres to phagocytes by surface modification with poly(L-lysine)-grafted poly(ethylene glycol) conjugate. Pharm Res. 2003 Feb;20(2):237-46. Pubmed: 12636162
  • Hagenfeldt L, Bjerkenstedt L, Edman G, Sedvall G, Wiesel FA: Amino acids in plasma and CSF and monoamine metabolites in CSF: interrelationship in healthy subjects. J Neurochem. 1984 Mar;42(3):833-7. Pubmed: 6198473
  • Hajishengallis G, Koga T, Russell MW: Affinity and specificity of the interactions between Streptococcus mutans antigen I/II and salivary components. J Dent Res. 1994 Sep;73(9):1493-502. Pubmed: 7523469
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • 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
  • Kranz BR: Detection of rare malignant cells and their apoptotic fragments in cerebrospinal fluid. Lancet. 2000 Oct 7;356(9237):1242-4. Pubmed: 11072949
  • Nicholson JK, O'Flynn MP, Sadler PJ, Macleod AF, Juul SM, Sonksen PH: Proton-nuclear-magnetic-resonance studies of serum, plasma and urine from fasting normal and diabetic subjects. Biochem J. 1984 Jan 15;217(2):365-75. Pubmed: 6696735
  • Pahler A, Parker J, Dekant W: Dose-dependent protein adduct formation in kidney, liver, and blood of rats and in human blood after perchloroethene inhalation. Toxicol Sci. 1999 Mar;48(1):5-13. Pubmed: 10330678
  • Peng CT, Wu KH, Lan SJ, Tsai JJ, Tsai FJ, Tsai CH: Amino acid concentrations in cerebrospinal fluid in children with acute lymphoblastic leukemia undergoing chemotherapy. Eur J Cancer. 2005 May;41(8):1158-63. Epub 2005 Apr 14. Pubmed: 15911239
  • Rainesalo S, Keranen T, Palmio J, Peltola J, Oja SS, Saransaari P: Plasma and cerebrospinal fluid amino acids in epileptic patients. Neurochem Res. 2004 Jan;29(1):319-24. Pubmed: 14992292
  • Silwood CJ, Lynch E, Claxson AW, Grootveld MC: 1H and (13)C NMR spectroscopic analysis of human saliva. J Dent Res. 2002 Jun;81(6):422-7. Pubmed: 12097436
  • Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
  • 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
  • Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
  • 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
Synthesis Reference: Rothstein, Morton. DL-Lysine-6-C14 and DL-a-aminoadipic acid-6-C14. Biochemical Preparations (1961), 8 85-8.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID18019
HMDB IDHMDB00182
Pubchem Compound ID5962
Kegg IDC00047
ChemSpider ID5747
WikipediaL-Lysine
BioCyc IDLYS
EcoCyc IDLYS
Ligand ExpoLYS_LFZW_DHZ3

Enzymes

General function:
Involved in catalytic activity
Specific function:
Meso-2,6-diaminoheptanedioate = L-lysine + CO(2)
Gene Name:
lysA
Locus Tag:
PA5277
Molecular weight:
45.5 kDa
Reactions
Meso-2,6-diaminoheptanedioate = L-lysine + CO(2).
General function:
Involved in nucleotide binding
Specific function:
Part of the binding-protein-dependent transport system for histidine. Probably responsible for energy coupling to the transport system
Gene Name:
hisP
Locus Tag:
PA2926
Molecular weight:
28.5 kDa
General function:
Involved in nucleotide binding
Specific function:
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
Gene Name:
lysS
Locus Tag:
PA3700
Molecular weight:
57.3 kDa
Reactions
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
General function:
Involved in nucleotide binding
Specific function:
With YjeK might be involved in the post-translational modification of elongation factor P (EF-P)
Gene Name:
poxA
Locus Tag:
PA5513
Molecular weight:
32.4 kDa
General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for histidine; probably responsible for the translocation of the substrate across the membrane
Gene Name:
hisM
Locus Tag:
PA2925
Molecular weight:
26.7 kDa
General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for histidine; probably responsible for the translocation of the substrate across the membrane
Gene Name:
hisQ
Locus Tag:
PA2924
Molecular weight:
24.5 kDa

Transporters

General function:
Involved in nucleotide binding
Specific function:
Part of the binding-protein-dependent transport system for histidine. Probably responsible for energy coupling to the transport system
Gene Name:
hisP
Locus Tag:
PA2926
Molecular weight:
28.5 kDa
General function:
Involved in nucleotide binding
Specific function:
Probably part of a binding-protein-dependent transport system yecCS for an amino acid. Probably responsible for energy coupling to the transport system
Gene Name:
yecC
Locus Tag:
PA5152
Molecular weight:
28.4 kDa
General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for histidine; probably responsible for the translocation of the substrate across the membrane
Gene Name:
hisM
Locus Tag:
PA2925
Molecular weight:
26.7 kDa
General function:
Involved in transport
Specific function:
Permease that is involved in the transport across the cytoplasmic membrane of lysine
Gene Name:
lysP
Locus Tag:
PA4628
Molecular weight:
53.1 kDa
General function:
Involved in transporter activity
Specific function:
Part of the binding-protein-dependent transport system for histidine; probably responsible for the translocation of the substrate across the membrane
Gene Name:
hisQ
Locus Tag:
PA2924
Molecular weight:
24.5 kDa