Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000497
Identification
Name: D-Serine
Description:Serine is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines. It is the precursor to several amino acids including glycine and cysteine, and tryptophan in bacteria. It is also the precursor to numerous of other metabolites, including sphingolipids and folate, which is the principal donor of one-carbon fragments in biosynthesis. Serine dehydratase is an enzyme that converts serine to pyruvate.
Structure
Thumb
Synonyms:
  • (2R)-2-amino-3-hydroxypropanoate
  • (2R)-2-amino-3-hydroxypropanoic acid
  • (R)-2-amino-3-hydroxypropanoate
  • (R)-2-amino-3-hydroxypropanoic acid
  • D-Ser
  • D-Serin
  • DL-Serine
  • DSN
  • Serine D-form
Chemical Formula: C3H7NO3
Average Molecular Weight: 105.0926
Monoisotopic Molecular Weight: 105.042593095
InChI Key: MTCFGRXMJLQNBG-UWTATZPHSA-N
InChI:InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
CAS number: 312-84-5
IUPAC Name:(2R)-2-amino-3-hydroxypropanoic acid
Traditional IUPAC Name: D-serine
SMILES:N[C@H](CO)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-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 D-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Beta-hydroxy acid
  • Hydroxy acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 229 °C
Experimental Properties:
PropertyValueSource
Water Solubility:364 mg/mL at 20 oC [BEILSTEIN]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility480.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.04 m3·mol-1ChemAxon
Polarizability9.39 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-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-9000000000-d33888cff00d0ade0ffeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-9000000000-f7e50afcb90768dce4a5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9000000000-043951ed5540cce44f4eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
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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.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID16523
HMDB IDHMDB03406
Pubchem Compound ID71077
Kegg IDC00740
ChemSpider ID64231
WikipediaDSN
BioCyc IDD-SERINE
EcoCyc IDD-SERINE
Ligand ExpoDSN

Enzymes

General function:
Involved in D-serine ammonia-lyase activity
Specific function:
D-serine = pyruvate + NH(3)
Gene Name:
dsdA
Locus Tag:
PA3357
Molecular weight:
48.2 kDa
Reactions
D-serine = pyruvate + NH(3).
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the NADP-dependent oxidation of L-allo- threonine to L-2-amino-3-keto-butyrate, which is spontaneously decarboxylated into aminoacetone. Also acts on L-serine, D-serine, D-threonine, D-3-hydroxyisobutyrate, L-3-hydroxyisobutyrate, D- glycerate and L-glycerate
Gene Name:
ydfG
Locus Tag:
PA4907
Molecular weight:
27.4 kDa
Reactions
3-hydroxypropanoate + NADP(+) = 3-oxopropanoate + NADPH.

Transporters

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 sodium:dicarboxylate symporter activity
Specific function:
Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system)
Gene Name:
sstT
Locus Tag:
PA2042
Molecular weight:
42.4 kDa