Basic Info

Common NameL-Serine(F05360)
2D Structure
Description

Serine is a nonessential amino acid derived from glycine. Like all the amino acid building blocks of protein and peptides, serine can become essential under certain conditions, and is thus important in maintaining health and preventing disease. Low-average concentration of serine compared to other amino acids is found in muscle. Serine is highly concentrated in all cell membranes. L-Serine may be derived from four possible sources: dietary intake; biosynthesis from the glycolytic intermediate 3-phosphoglycerate; from glycine ; and by protein and phospholipid degradation. Little data is available on the relative contributions of each of these four sources of l-serine to serine homoeostasis. It is very likely that the predominant source of l-serine will be very different in different tissues and during different stages of human development. In the biosynthetic pathway, the glycolytic intermediate 3-phosphoglycerate is converted into phosphohydroxypyruvate, in a reaction catalyzed by 3-phosphoglycerate dehydrogenase (3- PGDH; EC 1.1.1.95). Phosphohydroxypyruvate is metabolized to phosphoserine by phosphohydroxypyruvate aminotransferase (EC 2.6.1.52) and, finally, phosphoserine is converted into l-serine by phosphoserine phosphatase (PSP; EC 3.1.3.3). In liver tissue, the serine biosynthetic pathway is regulated in response to dietary and hormonal changes. Of the three synthetic enzymes, the properties of 3-PGDH and PSP are the best documented. Hormonal factors such as glucagon and corticosteroids also influence 3-PGDH and PSP activities in interactions dependent upon the diet. L-serine plays a central role in cellular proliferation. L-Serine is the predominant source of one-carbon groups for the de novo synthesis of purine nucleotides and deoxythymidine monophosphate. It has long been recognized that, in cell cultures, L-serine is a conditional essential amino acid, because it cannot be synthesized in sufficient quantities to meet the cellular demands for its utilization. In recent years, L-serine and the products of its metabolism have been recognized not only to be essential for cell proliferation, but also to be necessary for specific functions in the central nervous system. The findings of altered levels of serine and glycine in patients with psychiatric disorders and the severe neurological abnormalities in patients with defects of L-serine synthesis underscore the importance of L-serine in brain development and function. (A3449).

FRCD IDF05360
CAS Number56-45-1
PubChem CID5951
FormulaC3H7NO3
IUPAC Name

(2S)-2-amino-3-hydroxypropanoic acid

InChI Key

MTCFGRXMJLQNBG-REOHCLBHSA-N

InChI

InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1

Canonical SMILES

C(C(C(=O)O)N)O

Isomeric SMILES

C([C@@H](C(=O)O)N)O

WikipediaL-Serine
Synonyms
        
            L-(-)-Serine
        
            Polyserine
        
            L-serine
        
            serine
        
            56-45-1
        
            (S)-2-Amino-3-hydroxypropanoic acid
        
            (S)-Serine
        
            beta-Hydroxyalanine
        
            H-Ser-OH
        
            L-ser
        
Classifies
                

                  
                    Animal Toxin
                  

                
        
Update DateNov 13, 2018 17:07

Chemical Taxonomy

KingdomOrganic compounds
SuperclassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
SubclassAmino acids, peptides, and analogues
Intermediate Tree NodesAmino acids and derivatives - Alpha amino acids and derivatives
Direct ParentSerine and derivatives
Alternative Parents
Molecular FrameworkAliphatic acyclic compounds
SubstituentsSerine or derivatives - Alpha-amino acid - L-alpha-amino acid - Beta-hydroxy acid - Hydroxy acid - Amino acid - Carboxylic acid - Monocarboxylic acid or derivatives - Alcohol - Primary amine - Primary alcohol - Organooxygen compound - Organonitrogen compound - Hydrocarbon derivative - Primary aliphatic amine - Organic oxide - Organopnictogen compound - Carbonyl group - Organic oxygen compound - Amine - Organic nitrogen compound - Aliphatic acyclic compound
DescriptionThis compound belongs to the class of organic compounds known as serine and derivatives. These are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Properties

Property NameProperty Value
Molecular Weight105.093
Hydrogen Bond Donor Count3
Hydrogen Bond Acceptor Count4
Rotatable Bond Count2
Complexity72.6
Monoisotopic Mass105.043
Exact Mass105.043
XLogP-3.1
Formal Charge0
Heavy Atom Count7
Defined Atom Stereocenter Count1
Undefined Atom Stereocenter Count0
Defined Bond Stereocenter Count0
Undefined Bond Stereocenter Count0
Isotope Atom Count0
Covalently-Bonded Unit Count1

ADMET

Model Result Probability
Absorption
Blood-Brain BarrierBBB-0.6529
Human Intestinal AbsorptionHIA+0.9407
Caco-2 PermeabilityCaco2-0.7839
P-glycoprotein SubstrateNon-substrate0.7693
P-glycoprotein InhibitorNon-inhibitor0.9862
Non-inhibitor0.9877
Renal Organic Cation TransporterNon-inhibitor0.9436
Distribution
Subcellular localizationLysosome0.6959
Metabolism
CYP450 2C9 SubstrateNon-substrate0.8673
CYP450 2D6 SubstrateNon-substrate0.8460
CYP450 3A4 SubstrateNon-substrate0.8389
CYP450 1A2 InhibitorNon-inhibitor0.9087
CYP450 2C9 InhibitorNon-inhibitor0.9512
CYP450 2D6 InhibitorNon-inhibitor0.9349
CYP450 2C19 InhibitorNon-inhibitor0.9450
CYP450 3A4 InhibitorNon-inhibitor0.9080
CYP Inhibitory PromiscuityLow CYP Inhibitory Promiscuity0.9914
Excretion
Toxicity
Human Ether-a-go-go-Related Gene InhibitionWeak inhibitor0.9923
Non-inhibitor0.9811
AMES ToxicityNon AMES toxic0.9088
CarcinogensNon-carcinogens0.8200
Fish ToxicityLow FHMT0.8678
Tetrahymena Pyriformis ToxicityLow TPT0.9972
Honey Bee ToxicityLow HBT0.5782
BiodegradationReady biodegradable0.9489
Acute Oral ToxicityIII0.5142
Carcinogenicity (Three-class)Non-required0.7108

Model Value Unit
Absorption
Aqueous solubility0.1752LogS
Caco-2 Permeability-0.1022LogPapp, cm/s
Distribution
Metabolism
Excretion
Toxicity
Rat Acute Toxicity1.2700LD50, mol/kg
Fish Toxicity2.8128pLC50, mg/L
Tetrahymena Pyriformis Toxicity-1.0558pIGC50, ug/L

References

TitleJournalDatePubmed ID
Proteomic characterization of six Taiwanese snake venoms: Identification of species-specific proteins and development of a SISCAPA-MRM assay for cobra venom factors.J Proteomics2018 Sep 1529929037
Metabolic and proteomic mechanism of bisphenol A degradation by Bacillusthuringiensis.Sci Total Environ2018 Nov 129879660
The extracellular proteases produced by Vibrio parahaemolyticus.World J Microbiol Biotechnol2018 May 1129752585
Herpud1 impacts insulin-dependent glucose uptake in skeletal muscle cells bycontrolling the Ca2+-calcineurin-Akt axis.Biochim Biophys Acta2018 May29486284
Influence of the metal ion on the enzyme activity and kinetics of PepA fromLactobacillus delbrueckii.Enzyme Microb Technol2018 Mar29310858
Phosphorylation regulated by protein kinase A and alkaline phosphatase playpositive roles in μ-calpain activity.Food Chem2018 Jun 3029478550
Characterization of phenolics, amino acids, fatty acids and antioxidant activity in pulp and seeds of high altitude Himalayan crab apple fruits (Malus baccata).J Food Sci Technol2018 Jun29892117
Frequency of Mutations in Quinolone Resistance-Determining Regions andPlasmid-Mediated Quinolone Resistance in Shigella Isolates Recovered fromPediatric Patients in Tehran, Iran: An Overlooked Problem.Microb Drug Resist2018 Jul/Aug29148915
Exogenous short-term silicon application regulates macro-nutrients, endogenousphytohormones, and protein expression in Oryza sativa L.BMC Plant Biol2018 Jan 429301510
Altered Serum Metabolite Profiling and Relevant Pathway Analysis in Rats Stimulated by Honeybee Venom: New Insight into Allergy to Honeybee Venom.J Agric Food Chem2018 Jan 3129322776
Investigating the effect of dietary calcium levels on ileal endogenous amino acidlosses and standardized ileal amino acid digestibility in broilers and layinghens.Poult Sci2018 Jan 129077891
The involvement of suppressor of cytokine signaling 6 (SOCS6) in immune response of Chinese mitten crab Eriocheir sinensis.Fish Shellfish Immunol2018 Jan29155031
Roles of dietary glycine, proline, and hydroxyproline in collagen synthesis andanimal growth.Amino Acids2018 Jan28929384
Investigating the inhibitory potential of 2-Aminopurine metal complexes againstserine/threonine protein kinases from Mycobacterium tuberculosis.Tuberculosis (Edinb)2018 Jan29523327
Purification and characterization of fibrinolytic protease from Bacillusamyloliquefaciens MCC2606 and analysis of fibrin degradation product by MS/MS.Prep Biochem Biotechnol2018 Feb 729341842
Structure and function of cytoplasmic serine hydroxymethyltransferase from Pichiapastoris.Biochem Biophys Res Commun2018 Feb 529339156
Gas chromatography-mass spectrometry metabolomic study of lipopolysaccharides toxicity on rat basophilic leukemia cells.Chem Biol Interact2018 Feb 129275087
Influence of structural and surface properties of whey-derived peptides onzinc-chelating capacity, and in vitro gastric stability and bioaccessibility ofthe zinc-peptide complexes.Food Chem2018 Feb 128946246
A novel galactolipase from a green microalga Chlorella kessleri: purification,characterization, molecular cloning, and heterologous expression.Appl Microbiol Biotechnol2018 Feb29299622
Physicochemical and sensory properties of yogurts containing sacha inchi(Plukenetia volubilis L.) seeds and β-glucans from Ganoderma lucidum.J Dairy Sci2018 Feb29153530

Targets

General Function:
Pyridoxal phosphate binding
Gene Name:
SDS
Uniprot ID:
P20132
Molecular Weight:
34625.105 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [17139284 ]
General Function:
Transaminase activity
Gene Name:
AGXT
Uniprot ID:
P21549
Molecular Weight:
43009.535 Da
References
  1. Yard BA, Carter LG, Johnson KA, Overton IM, Dorward M, Liu H, McMahon SA, Oke M, Puech D, Barton GJ, Naismith JH, Campopiano DJ: The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol. 2007 Jul 27;370(5):870-86. Epub 2007 May 10. [17559874 ]
General Function:
Threonine racemase activity
Specific Function:
Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.
Gene Name:
SRR
Uniprot ID:
Q9GZT4
Molecular Weight:
36565.905 Da
References
  1. Fujitani Y, Horiuchi T, Ito K, Sugimoto M: Serine racemases from barley, Hordeum vulgare L., and other plant species represent a distinct eukaryotic group: gene cloning and recombinant protein characterization. Phytochemistry. 2007 Jun;68(11):1530-6. Epub 2007 May 17. [17499824 ]
General Function:
L-proline transmembrane transporter activity
Specific Function:
Neutral amino acid/proton symporter. Has a pH-dependent electrogenic transport activity for small amino acids such as glycine, alanine and proline. Besides small apolar L-amino acids, it also recognize their D-enantiomers and selected amino acid derivatives such as gamma-aminobutyric acid (By similarity).
Gene Name:
SLC36A1
Uniprot ID:
Q7Z2H8
Molecular Weight:
53075.045 Da
References
  1. Thondorf I, Voigt V, Schafer S, Gebauer S, Zebisch K, Laug L, Brandsch M: Three-dimensional quantitative structure-activity relationship analyses of substrates of the human proton-coupled amino acid transporter 1 (hPAT1). Bioorg Med Chem. 2011 Nov 1;19(21):6409-18. doi: 10.1016/j.bmc.2011.08.058. Epub 2011 Sep 5. [21955456 ]
General Function:
Serine c-palmitoyltransferase activity
Specific Function:
Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference.
Gene Name:
SPTLC1
Uniprot ID:
O15269
Molecular Weight:
52743.41 Da
References
  1. Yard BA, Carter LG, Johnson KA, Overton IM, Dorward M, Liu H, McMahon SA, Oke M, Puech D, Barton GJ, Naismith JH, Campopiano DJ: The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol. 2007 Jul 27;370(5):870-86. Epub 2007 May 10. [17559874 ]
General Function:
Serine c-palmitoyltransferase activity
Specific Function:
Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate.
Gene Name:
SPTLC2
Uniprot ID:
O15270
Molecular Weight:
62923.765 Da
References
  1. Yard BA, Carter LG, Johnson KA, Overton IM, Dorward M, Liu H, McMahon SA, Oke M, Puech D, Barton GJ, Naismith JH, Campopiano DJ: The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol. 2007 Jul 27;370(5):870-86. Epub 2007 May 10. [17559874 ]
General Function:
Serine-trna ligase activity
Specific Function:
Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).
Gene Name:
SARS
Uniprot ID:
P49591
Molecular Weight:
58776.785 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [17139284 ]
General Function:
Ubiquitin protein ligase binding
Specific Function:
Hydro-lyase catalyzing the first step of the transsulfuration pathway, where the hydroxyl group of L-serine is displaced by L-homocysteine in a beta-replacement reaction to form L-cystathionine, the precursor of L-cysteine. This catabolic route allows the elimination of L-methionine and the toxic metabolite L-homocysteine (PubMed:23981774, PubMed:20506325, PubMed:23974653). Also involved in the production of hydrogen sulfide, a gasotransmitter with signaling and cytoprotective effects on neurons (By similarity).
Gene Name:
CBS
Uniprot ID:
P35520
Molecular Weight:
60586.05 Da
References
  1. Sen S, Banerjee R: A pathogenic linked mutation in the catalytic core of human cystathionine beta-synthase disrupts allosteric regulation and allows kinetic characterization of a full-length dimer. Biochemistry. 2007 Apr 3;46(13):4110-6. Epub 2007 Mar 13. [17352495 ]