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D-Serine (YMDB00284)

Identification
YMDB IDYMDB00284
NameD-Serine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionD-Serine, also known as D-serin or DSN, belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives 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. D-Serine is a very strong basic compound (based on its pKa). D-Serine exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (2R)-2-amino-3-hydroxypropanoate
  • (2R)-2-amino-3-hydroxypropanoic acid
  • (R)-2-amino-3-hydroxypropanoate
  • (R)-2-amino-3-hydroxypropanoic acid
  • D-Serin
  • DL-Serine
  • DSN
  • Serine D-form
  • (R)-2-Amino-3-hydroxy-propionic acid
  • (R)-2-Amino-3-hydroxy-propionate
CAS number312-84-5
WeightAverage: 105.0926
Monoisotopic: 105.042593095
InChI KeyMTCFGRXMJLQNBG-UWTATZPHSA-N
InChIInChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
IUPAC Name(2R)-2-amino-3-hydroxypropanoic acid
Traditional IUPAC NameD-serine
Chemical FormulaC3H7NO3
SMILES[H]OC(=O)[C@]([H])(N([H])[H])C([H])([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives 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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentSerine and derivatives
Alternative Parents
Substituents
  • Serine or derivatives
  • Alpha-amino acid
  • D-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
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point228 °C
Experimental Properties
PropertyValueReference
Water Solubility425 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP-3.07 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility480 g/LALOGPS
logP-3.4ALOGPS
logP-3.9ChemAxon
logS0.66ALOGPS
pKa (Strongest Acidic)2.03ChemAxon
pKa (Strongest Basic)8.93ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.04 m³·mol⁻¹ChemAxon
Polarizability9.39 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG Pathways
Glycine, serine and threonine metabolismec00260 Map00260
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-06sl-9000000000-033631650075b940e0e2JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0089-9810000000-06fed7f6e260b107d95aJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-9000000000-d33888cff00d0ade0ffeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-9000000000-f7e50afcb90768dce4a5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9000000000-043951ed5540cce44f4eJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-6900000000-ee98a5a83ffbd434740eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0uki-9200000000-fa8d04d6ce99a290d187JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05fu-9000000000-001b18464fb313594decJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-9100000000-113290360f404e0abfe6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-9000000000-a5d4e47e8a548414bcb5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0596-9000000000-45f597b943c27fee51e7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-08g0-9300000000-dab8446816db786db171JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-9000000000-1a5aef91299ef3583ca2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-b6cfe52e68c644cacfd7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-9000000000-c00dff763ff1f56fda00JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9000000000-980e3923ad0861629a12JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-90338875078d415c5036JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
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
  • Yow, G. Y., Uo, T., Yoshimura, T., Esaki, N. (2004). "D-amino acid N-acetyltransferase of Saccharomyces cerevisiae: a close homologue of histone acetyltransferase Hpa2p acting exclusively on free D-amino acids." Arch Microbiol 182:396-403.15375647
  • Cowart, L. A., Hannun, Y. A. (2005). "Using genomic and lipidomic strategies to investigate sphingolipid function in the yeast heat-stress response." Biochem Soc Trans 33:1166-1169.16246073
Synthesis Reference:Zhu, Yanxin; Yuan, Minglong; Yuan, Mingwei; Du, Bilin; Zheng, Ling. Preparation of D-serine from acetylglycine. Faming Zhuanli Shenqing Gongkai Shuomingshu (2006), 4pp.
External Links:
ResourceLink
CHEBI ID16523
HMDB IDHMDB03406
Pubchem Compound ID71077
Kegg IDC00740
ChemSpider ID64231
FOODB IDFDB023164
WikipediaSerine
BioCyc IDSerines

Enzymes

Protein Details
1. N-acetyltransferase HPA3
General function:
Involved in N-acetyltransferase activity
Specific function:
N-acetyltransferase whose physiological acetyl acceptor substrate is still unknown. In vitro, histone acetylation is very weak
Gene Name:
HPA3
Uniprot ID:
P39979
Molecular weight:
20698.5
Reactions
acetyl-CoA + a D-amino acid → CoA + an N-acetyl-D-amino acid
Protein Details
2. D-serine dehydratase
General function:
Involved in D-serine ammonia-lyase activity
Specific function:
Converts specifically D-serine to pyruvate and ammonia. May play a role in D-serine detoxification
Gene Name:
DSD1
Uniprot ID:
P53095
Molecular weight:
47827.39844
Reactions
D-serine → pyruvate + NH(3).