Showing Compound Card for D-Serine (CDB004957)

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Record Information
Version1.0
Created at2020-04-17 18:54:27 UTC
Updated at2020-12-07 19:11:22 UTC
CannabisDB IDCDB004957
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameD-Serine
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. D-serine can be biosynthesized from L-serine through the action of the enzyme serine racemase. In humans, D-serine is involved in the metabolic disorder called non-ketotic hyperglycinemia. Outside of the human body, D-Serine has been detected, but not quantified in, several different foods, such as persian limes, mustard spinachs, black mulberries, epazotes, and wheats. This could make D-serine a potential biomarker for the consumption of these foods. The R-enantiomer of serine. D-Serine is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(2R)-2-Amino-3-hydroxypropanoic acidChEBI
(R)-2-Amino-3-hydroxy-propionic acidChEBI
(R)-2-Amino-3-hydroxypropanoic acidChEBI
D-SerinChEBI
DSNChEBI
(2R)-2-Amino-3-hydroxypropanoateGenerator
(R)-2-Amino-3-hydroxy-propionateGenerator
(R)-2-Amino-3-hydroxypropanoateGenerator
DL-SerineHMDB
Serine D-formHMDB
Chemical FormulaC3H7NO3
Average Molecular Weight105.09
Monoisotopic Molecular Weight105.0426
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 KeyMTCFGRXMJLQNBG-UWTATZPHSA-N
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
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

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
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSD-Serine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-06sl-9000000000-033631650075b940e0e2Spectrum
Predicted GC-MSD-Serine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0089-9810000000-06fed7f6e260b107d95aSpectrum
Predicted GC-MSD-Serine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-9000000000-d33888cff00d0ade0ffe2012-07-25View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-9000000000-f7e50afcb90768dce4a52012-07-25View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9000000000-043951ed5540cce44f4e2012-07-25View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-6900000000-ee98a5a83ffbd434740e2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0uki-9200000000-fa8d04d6ce99a290d1872016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05fu-9000000000-001b18464fb313594dec2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-9100000000-113290360f404e0abfe62021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-9000000000-a5d4e47e8a548414bcb52021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0596-9000000000-45f597b943c27fee51e72021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-08g0-9300000000-dab8446816db786db1712016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-9000000000-1a5aef91299ef3583ca22016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-b6cfe52e68c644cacfd72016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-9000000000-c00dff763ff1f56fda002021-09-23View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9000000000-980e3923ad0861629a122021-09-23View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-90338875078d415c50362021-09-23View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)Spectrum
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
Phosphoserine phosphatasePSPH7p11.2P78330 details
Serine racemaseSRR17p13Q9GZT4 details
Transporters
Protein NameGene NameLocusUniprot IDDetails
Asc-type amino acid transporter 1SLC7A1019q13.1Q9NS82 details
Metal BindingsNot Available
ReceptorsNot Available
Transcriptional FactorsNot Available
Concentrations Data
Cannabis CultivarStatusValueReferenceDetails
Alien DawgDetected and Quantified0.55 mg/g dry wt
    • David S. Wishart,...
 details
Sensi StarDetected and Quantified0.39 mg/g dry wt
    • David S. Wishart,...
 details
Tangerine DreamDetected and Quantified0.62 mg/g dry wt
    • David S. Wishart,...
 details
HMDB IDHMDB0003406
DrugBank IDDB03929
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023164
KNApSAcK IDNot Available
Chemspider ID64231
KEGG Compound IDC00740
BioCyc IDD-SERINE
BiGG ID35846
Wikipedia LinkSerine
METLIN ID6920
PubChem Compound71077
PDB IDNot Available
ChEBI ID16523
References
General ReferencesNot Available

Enzymes

Enzyme Details
1. Phosphoserine phosphatase
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
Enzyme Details
2. Serine racemase
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

Transporters

Enzyme Details
1. Asc-type amino acid transporter 1
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