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Record Information
Version3.6
Creation Date2006-08-12 20:15:26 UTC
Update Date2016-10-12 16:27:30 UTC
HMDB IDHMDB03406
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-Serine
DescriptionD-serine is a stereo-isomer of the common amino acid, L-serine. D-serine was only thought to exist in bacteria until relatively recently. D-serine was the second D amino acid discovered to naturally exist in humans. The first one was D-aspartate. D-serine is synthesized from L-serine by serine racemase (SRR), and it is degraded by D-amino acid oxidase (DAO). It is found in high abundance in the brain. D-serine acts on the glycine binding site of the N-methyl-D-aspartate receptor (NMDAR) and modulates glutamate-mediated receptor activation. For the receptor to open, glutamate and either glycine or D-serine must bind to it. In fact, D-serine is a more potent agonist at the glycine site on the NMDAR than glycine itself. The importance of D-serine in mammalian brain function is apparent from extensive investigations reported and reviewed over the past decade, including roles in synaptic plasticity and memory. D-serine is also implicated in the pathophysiology and therapy of several psychiatric and neurological conditions including schizophrenia and glioma. In schizophrenia, there is evidence that D-serine levels are decreased, a deficiency that may contribute to the proposed NMDAR hypofunction of the disorder and that has led to D-serine replenishment as a novel therapeutic strategy.
Structure
Thumb
Synonyms
ValueSource
(2R)-2-amino-3-Hydroxypropanoic acidChEBI
(R)-2-amino-3-Hydroxy-propionic acidChEBI
(R)-2-amino-3-Hydroxypropanoic acidChEBI
D-SerinChEBI
(2R)-2-amino-3-HydroxypropanoateGenerator
(R)-2-amino-3-Hydroxy-propionateGenerator
(R)-2-amino-3-HydroxypropanoateGenerator
DL-SerineHMDB
DSNHMDB
Serine D-formHMDB
Chemical FormulaC3H7NO3
Average Molecular Weight105.0926
Monoisotopic Molecular Weight105.042593095
IUPAC Name(2R)-2-amino-3-hydroxypropanoic acid
Traditional NameD-serine
CAS Registry Number312-84-5
SMILES
N[C@H](CO)C(O)=O
InChI Identifier
InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
InChI KeyInChIKey=MTCFGRXMJLQNBG-UWTATZPHSA-N
Chemical 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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentD-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 FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Glycine, serine and threonine metabolism
ApplicationNot Available
Cellular locations
  • Extracellular
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point229 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility364 mg/mL at 20 °CNot Available
LogPNot AvailableNot Available
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
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-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
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue Location
  • Adipose Tissue
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Lung
  • Muscle
  • Myelin
  • Neuron
  • Pancreas
  • Placenta
  • Platelet
  • Prostate
  • Skeletal Muscle
  • Spleen
  • Stratum Corneum
  • Testes
Pathways
NameSMPDB LinkKEGG Link
3-Phosphoglycerate dehydrogenase deficiencySMP00721Not Available
Amikacin PathwaySMP00253Not Available
Arbekacin Action PathwaySMP00713Not Available
Azithromycin PathwaySMP00247Not Available
Chloramphenicol Action PathwaySMP00729Not Available
Clarithromycin PathwaySMP00248Not Available
Clindamycin PathwaySMP00249Not Available
Clomocycline PathwaySMP00262Not Available
Demeclocycline PathwaySMP00290Not Available
Dihydropyrimidine Dehydrogenase Deficiency (DHPD)SMP00179Not Available
Dimethylglycine Dehydrogenase DeficiencySMP00242Not Available
Dimethylglycine Dehydrogenase DeficiencySMP00484Not Available
Doxycycline PathwaySMP00291Not Available
Erythromycin PathwaySMP00250Not Available
Gentamicin PathwaySMP00254Not Available
Glycine and Serine MetabolismSMP00004map00260
Hyperglycinemia, non-ketoticSMP00485Not Available
Josamycin Action PathwaySMP00731Not Available
Kanamycin PathwaySMP00255Not Available
Lincomycin Action PathwaySMP00728Not Available
Lymecycline PathwaySMP00295Not Available
Methacycline Action PathwaySMP00727Not Available
Minocycline PathwaySMP00292Not Available
Neomycin PathwaySMP00256Not Available
Netilmicin PathwaySMP00257Not Available
Non Ketotic HyperglycinemiaSMP00223Not Available
Oxytetracycline PathwaySMP00293Not Available
Paromomycin Action PathwaySMP00714Not Available
Rolitetracycline Action PathwaySMP00726Not Available
Roxithromycin PathwaySMP00251Not Available
SarcosinemiaSMP00244Not Available
Spectinomycin PathwaySMP00258Not Available
Streptomycin PathwaySMP00259Not Available
Telithromycin PathwaySMP00252Not Available
Tetracycline PathwaySMP00294Not Available
Tigecycline Action PathwaySMP00712Not Available
Tobramycin Action PathwaySMP00711Not Available
Transcription/TranslationSMP00019Not Available
Troleandomycin Action PathwaySMP00730Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1.88 +/- 0.07 uMAdult (>18 years old)Both
Normal
details
BloodDetected and Quantified2.28 +/- 0.59 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified3.6 +/- 2.2 uMAdult (>18 years old)MaleNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified52.0 (25.0-105.0) uMAdult (>18 years old)BothNormal details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
UrineDetected and Quantified0.0021 - 10.1 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1.57 +/- 0.07 uMAdult (>18 years old)Both
Schizophrenia
details
BloodDetected and Quantified1.86 +/- 0.53 uMAdult (>18 years old)BothSchizophrenia details
UrineDetected and Quantified0.0041 - 0.0122 umol/mmol creatinineAdult (>18 years old)BothADPKD details
Associated Disorders and Diseases
Disease References
Schizophrenia
  1. Hashimoto K, Fukushima T, Shimizu E, Komatsu N, Watanabe H, Shinoda N, Nakazato M, Kumakiri C, Okada S, Hasegawa H, Imai K, Iyo M: Decreased serum levels of D-serine in patients with schizophrenia: evidence in support of the N-methyl-D-aspartate receptor hypofunction hypothesis of schizophrenia. Arch Gen Psychiatry. 2003 Jun;60(6):572-6. [12796220 ]
  2. Fukushima T, Iizuka H, Yokota A, Suzuki T, Ohno C, Kono Y, Nishikiori M, Seki A, Ichiba H, Watanabe Y, Hongo S, Utsunomiya M, Nakatani M, Sadamoto K, Yoshio T: Quantitative analyses of schizophrenia-associated metabolites in serum: serum D-lactate levels are negatively correlated with gamma-glutamylcysteine in medicated schizophrenia patients. PLoS One. 2014 Jul 8;9(7):e101652. doi: 10.1371/journal.pone.0101652. eCollection 2014. [25004141 ]
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB023164
KNApSAcK IDNot Available
Chemspider ID64231
KEGG Compound IDC00740
BioCyc IDSerines
BiGG ID35846
Wikipedia LinkDSN
NuGOwiki LinkHMDB03406
Metagene LinkHMDB03406
METLIN ID6920
PubChem Compound71077
PDB IDDSN
ChEBI ID16523
References
Synthesis ReferenceZhu, 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)
General References
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Enzymes

General function:
Involved in catalytic activity
Specific function:
Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.
Gene Name:
PSPH
Uniprot ID:
P78330
Molecular weight:
25007.49
General function:
Amino acid transport and metabolism
Specific function:
Sodium-independent, high affinity transport of small neutral D- and L-amino acids. May play a role in the modulation of glutamatergic transmission through mobilization of D-serine at the glutamatergic synapse
Gene Name:
SLC7A10
Uniprot ID:
Q9NS82
Molecular weight:
56797.4
General function:
Involved in catalytic 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
Reactions
L-Serine → D-Serinedetails
D-Serine → Pyruvic acid + Ammoniadetails