L-Serine
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Basic Info
Common Name | L-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 ID | F05360 |
CAS Number | 56-45-1 |
PubChem CID | 5951 |
Formula | C3H7NO3 |
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 |
Wikipedia | L-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 Date | Nov 13, 2018 17:07 |
Chemical Taxonomy
Kingdom | Organic compounds |
Superclass | Organic acids and derivatives |
Class | Carboxylic acids and derivatives |
Subclass | Amino acids, peptides, and analogues |
Intermediate Tree Nodes | Amino acids and derivatives - Alpha amino acids and derivatives |
Direct Parent | Serine and derivatives |
Alternative Parents | |
Molecular Framework | Aliphatic acyclic compounds |
Substituents | Serine 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 |
Description | This 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 Name | Property Value |
---|---|
Molecular Weight | 105.093 |
Hydrogen Bond Donor Count | 3 |
Hydrogen Bond Acceptor Count | 4 |
Rotatable Bond Count | 2 |
Complexity | 72.6 |
Monoisotopic Mass | 105.043 |
Exact Mass | 105.043 |
XLogP | -3.1 |
Formal Charge | 0 |
Heavy Atom Count | 7 |
Defined Atom Stereocenter Count | 1 |
Undefined Atom Stereocenter Count | 0 |
Defined Bond Stereocenter Count | 0 |
Undefined Bond Stereocenter Count | 0 |
Isotope Atom Count | 0 |
Covalently-Bonded Unit Count | 1 |
ADMET
Model | Result | Probability |
---|---|---|
Absorption | ||
Blood-Brain Barrier | BBB- | 0.6529 |
Human Intestinal Absorption | HIA+ | 0.9407 |
Caco-2 Permeability | Caco2- | 0.7839 |
P-glycoprotein Substrate | Non-substrate | 0.7693 |
P-glycoprotein Inhibitor | Non-inhibitor | 0.9862 |
Non-inhibitor | 0.9877 | |
Renal Organic Cation Transporter | Non-inhibitor | 0.9436 |
Distribution | ||
Subcellular localization | Lysosome | 0.6959 |
Metabolism | ||
CYP450 2C9 Substrate | Non-substrate | 0.8673 |
CYP450 2D6 Substrate | Non-substrate | 0.8460 |
CYP450 3A4 Substrate | Non-substrate | 0.8389 |
CYP450 1A2 Inhibitor | Non-inhibitor | 0.9087 |
CYP450 2C9 Inhibitor | Non-inhibitor | 0.9512 |
CYP450 2D6 Inhibitor | Non-inhibitor | 0.9349 |
CYP450 2C19 Inhibitor | Non-inhibitor | 0.9450 |
CYP450 3A4 Inhibitor | Non-inhibitor | 0.9080 |
CYP Inhibitory Promiscuity | Low CYP Inhibitory Promiscuity | 0.9914 |
Excretion | ||
Toxicity | ||
Human Ether-a-go-go-Related Gene Inhibition | Weak inhibitor | 0.9923 |
Non-inhibitor | 0.9811 | |
AMES Toxicity | Non AMES toxic | 0.9088 |
Carcinogens | Non-carcinogens | 0.8200 |
Fish Toxicity | Low FHMT | 0.8678 |
Tetrahymena Pyriformis Toxicity | Low TPT | 0.9972 |
Honey Bee Toxicity | Low HBT | 0.5782 |
Biodegradation | Ready biodegradable | 0.9489 |
Acute Oral Toxicity | III | 0.5142 |
Carcinogenicity (Three-class) | Non-required | 0.7108 |
Model | Value | Unit |
---|---|---|
Absorption | ||
Aqueous solubility | 0.1752 | LogS |
Caco-2 Permeability | -0.1022 | LogPapp, cm/s |
Distribution | ||
Metabolism | ||
Excretion | ||
Toxicity | ||
Rat Acute Toxicity | 1.2700 | LD50, mol/kg |
Fish Toxicity | 2.8128 | pLC50, mg/L |
Tetrahymena Pyriformis Toxicity | -1.0558 | pIGC50, ug/L |
References
Title | Journal | Date | Pubmed 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 Proteomics | 2018 Sep 15 | 29929037 |
Metabolic and proteomic mechanism of bisphenol A degradation by Bacillusthuringiensis. | Sci Total Environ | 2018 Nov 1 | 29879660 |
The extracellular proteases produced by Vibrio parahaemolyticus. | World J Microbiol Biotechnol | 2018 May 11 | 29752585 |
Herpud1 impacts insulin-dependent glucose uptake in skeletal muscle cells bycontrolling the Ca2+-calcineurin-Akt axis. | Biochim Biophys Acta | 2018 May | 29486284 |
Influence of the metal ion on the enzyme activity and kinetics of PepA fromLactobacillus delbrueckii. | Enzyme Microb Technol | 2018 Mar | 29310858 |
Phosphorylation regulated by protein kinase A and alkaline phosphatase playpositive roles in μ-calpain activity. | Food Chem | 2018 Jun 30 | 29478550 |
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 Technol | 2018 Jun | 29892117 |
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 Resist | 2018 Jul/Aug | 29148915 |
Exogenous short-term silicon application regulates macro-nutrients, endogenousphytohormones, and protein expression in Oryza sativa L. | BMC Plant Biol | 2018 Jan 4 | 29301510 |
Altered Serum Metabolite Profiling and Relevant Pathway Analysis in Rats Stimulated by Honeybee Venom: New Insight into Allergy to Honeybee Venom. | J Agric Food Chem | 2018 Jan 31 | 29322776 |
Investigating the effect of dietary calcium levels on ileal endogenous amino acidlosses and standardized ileal amino acid digestibility in broilers and layinghens. | Poult Sci | 2018 Jan 1 | 29077891 |
The involvement of suppressor of cytokine signaling 6 (SOCS6) in immune response of Chinese mitten crab Eriocheir sinensis. | Fish Shellfish Immunol | 2018 Jan | 29155031 |
Roles of dietary glycine, proline, and hydroxyproline in collagen synthesis andanimal growth. | Amino Acids | 2018 Jan | 28929384 |
Investigating the inhibitory potential of 2-Aminopurine metal complexes againstserine/threonine protein kinases from Mycobacterium tuberculosis. | Tuberculosis (Edinb) | 2018 Jan | 29523327 |
Purification and characterization of fibrinolytic protease from Bacillusamyloliquefaciens MCC2606 and analysis of fibrin degradation product by MS/MS. | Prep Biochem Biotechnol | 2018 Feb 7 | 29341842 |
Structure and function of cytoplasmic serine hydroxymethyltransferase from Pichiapastoris. | Biochem Biophys Res Commun | 2018 Feb 5 | 29339156 |
Gas chromatography-mass spectrometry metabolomic study of lipopolysaccharides toxicity on rat basophilic leukemia cells. | Chem Biol Interact | 2018 Feb 1 | 29275087 |
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 Chem | 2018 Feb 1 | 28946246 |
A novel galactolipase from a green microalga Chlorella kessleri: purification,characterization, molecular cloning, and heterologous expression. | Appl Microbiol Biotechnol | 2018 Feb | 29299622 |
Physicochemical and sensory properties of yogurts containing sacha inchi(Plukenetia volubilis L.) seeds and β-glucans from Ganoderma lucidum. | J Dairy Sci | 2018 Feb | 29153530 |
Targets
- General Function:
- Transaminase activity
- Gene Name:
- AGXT
- Uniprot ID:
- P21549
- Molecular Weight:
- 43009.535 Da
References
- 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
- 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
- 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
- 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
- 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
- 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
- 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 ]