Bovine Metabolome Database: Showing metabocard for D-Serine (BMDB0003406)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:04:20 UTC

Update Date

2020-05-19 22:01:35 UTC

BMDB ID

BMDB0003406

Secondary Accession Numbers

BMDB03406

Metabolite Identification

Common Name

D-Serine

Description

D-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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2R)-2-Amino-3-hydroxypropanoic acid	ChEBI
(R)-2-Amino-3-hydroxy-propionic acid	ChEBI
(R)-2-Amino-3-hydroxypropanoic acid	ChEBI
D-Serin	ChEBI
DSN	ChEBI
(2R)-2-Amino-3-hydroxypropanoate	Generator
(R)-2-Amino-3-hydroxy-propionate	Generator
(R)-2-Amino-3-hydroxypropanoate	Generator
DL-Serine	HMDB
Serine D-form	HMDB

Chemical Formula

C₃H₇NO₃

Average Molecular Weight

105.0926

Monoisotopic Molecular Weight

105.042593095

IUPAC Name

(2R)-2-amino-3-hydroxypropanoic acid

Traditional Name

D-serine

CAS Registry Number

312-84-5

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 Key

MTCFGRXMJLQNBG-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Serine 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 Framework

Aliphatic acyclic compounds

External Descriptors

D-alpha-amino acid (CHEBI:16523 )
serine (CHEBI:16523 )
Other amino acids (C00740 )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Myelin sheath

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	229 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	364 mg/mL at 20 °C	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-3.4	ALOGPS
logP	-3.9	ChemAxon
logS	0.66	ALOGPS
pKa (Strongest Acidic)	2.03	ChemAxon
pKa (Strongest Basic)	8.93	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	83.55 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	22.04 m³·mol⁻¹	ChemAxon
Polarizability	9.39 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-06sl-9000000000-033631650075b940e0e2	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0089-9810000000-06fed7f6e260b107d95a	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-9000000000-d33888cff00d0ade0ffe	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-9000000000-f7e50afcb90768dce4a5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0006-9000000000-043951ed5540cce44f4e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-6900000000-ee98a5a83ffbd434740e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0uki-9200000000-fa8d04d6ce99a290d187	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05fu-9000000000-001b18464fb313594dec	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-9100000000-113290360f404e0abfe6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-9000000000-a5d4e47e8a548414bcb5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0596-9000000000-45f597b943c27fee51e7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-08g0-9300000000-dab8446816db786db171	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-9000000000-1a5aef91299ef3583ca2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-b6cfe52e68c644cacfd7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-9000000000-c00dff763ff1f56fda00	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9000000000-980e3923ad0861629a12	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-90338875078d415c5036	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
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)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Myelin sheath

Biospecimen Locations

Adipose Tissue
Epidermis
Fibroblasts
Intestine
Kidney
Liver
Lung
Mammary Gland
Neuron
Pancreas
Placenta
Platelet
Prostate Tissue
Skeletal Muscle
Spleen
Testis

Pathways

Name	SMPDB/Pathwhiz	KEGG
Glycine and Serine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Adipose Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Lung	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Pancreas	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Testis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0003406

DrugBank ID

DB03929

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023164

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

16523

References

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)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Serine racemase

General function:: Amino acid transport and metabolism
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 (By similarity).
Gene Name:: SRR
Uniprot ID:: A0JNI4
Molecular weight:: 36181.0

Reactions

L-Serine → D-Serine	details

Showing metabocard for D-Serine (BMDB0003406)

Structure for BMDB0003406 (D-Serine)

Enzymes

Reactions