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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-08-12 20:15:26 UTC

Update Date

2021-09-14 15:00:09 UTC

HMDB ID

HMDB0003406

Secondary Accession Numbers

HMDB03406

Metabolite Identification

Common Name

D-Serine

Description

D-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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

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

Not Available

Physical Properties

State

Solid

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	480 g/L	ALOGPS
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	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	120.08	31661259
DarkChem	[M-H]-	114.376	31661259
DeepCCS	[M+H]+	117.869	30932474
DeepCCS	[M-H]-	115.069	30932474
DeepCCS	[M-2H]-	151.483	30932474
DeepCCS	[M+Na]+	126.183	30932474
AllCCS	[M+H]+	127.6	32859911
AllCCS	[M+H-H2O]+	123.3	32859911
AllCCS	[M+NH4]+	131.6	32859911
AllCCS	[M+Na]+	132.8	32859911
AllCCS	[M-H]-	120.3	32859911
AllCCS	[M+Na-2H]-	124.2	32859911
AllCCS	[M+HCOO]-	128.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Serine	N[C@H](CO)C(O)=O	2030.7	Standard polar	33892256
D-Serine	N[C@H](CO)C(O)=O	1098.5	Standard non polar	33892256
D-Serine	N[C@H](CO)C(O)=O	1623.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Serine,1TMS,isomer #1	C[Si](C)(C)OC[C@@H](N)C(=O)O	1208.8	Semi standard non polar	33892256
D-Serine,1TMS,isomer #2	C[Si](C)(C)OC(=O)[C@H](N)CO	1132.8	Semi standard non polar	33892256
D-Serine,1TMS,isomer #3	C[Si](C)(C)N[C@H](CO)C(=O)O	1262.0	Semi standard non polar	33892256
D-Serine,2TMS,isomer #1	C[Si](C)(C)OC[C@@H](N)C(=O)O[Si](C)(C)C	1244.3	Semi standard non polar	33892256
D-Serine,2TMS,isomer #2	C[Si](C)(C)N[C@H](CO[Si](C)(C)C)C(=O)O	1320.0	Semi standard non polar	33892256
D-Serine,2TMS,isomer #3	C[Si](C)(C)N[C@H](CO)C(=O)O[Si](C)(C)C	1293.4	Semi standard non polar	33892256
D-Serine,2TMS,isomer #4	C[Si](C)(C)N([C@H](CO)C(=O)O)[Si](C)(C)C	1465.7	Semi standard non polar	33892256
D-Serine,3TMS,isomer #1	C[Si](C)(C)N[C@H](CO[Si](C)(C)C)C(=O)O[Si](C)(C)C	1376.7	Semi standard non polar	33892256
D-Serine,3TMS,isomer #1	C[Si](C)(C)N[C@H](CO[Si](C)(C)C)C(=O)O[Si](C)(C)C	1408.1	Standard non polar	33892256
D-Serine,3TMS,isomer #1	C[Si](C)(C)N[C@H](CO[Si](C)(C)C)C(=O)O[Si](C)(C)C	1459.9	Standard polar	33892256
D-Serine,3TMS,isomer #2	C[Si](C)(C)OC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1510.6	Semi standard non polar	33892256
D-Serine,3TMS,isomer #2	C[Si](C)(C)OC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1454.5	Standard non polar	33892256
D-Serine,3TMS,isomer #2	C[Si](C)(C)OC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1587.0	Standard polar	33892256
D-Serine,3TMS,isomer #3	C[Si](C)(C)OC(=O)[C@@H](CO)N([Si](C)(C)C)[Si](C)(C)C	1470.0	Semi standard non polar	33892256
D-Serine,3TMS,isomer #3	C[Si](C)(C)OC(=O)[C@@H](CO)N([Si](C)(C)C)[Si](C)(C)C	1391.6	Standard non polar	33892256
D-Serine,3TMS,isomer #3	C[Si](C)(C)OC(=O)[C@@H](CO)N([Si](C)(C)C)[Si](C)(C)C	1542.5	Standard polar	33892256
D-Serine,4TMS,isomer #1	C[Si](C)(C)OC[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1565.7	Semi standard non polar	33892256
D-Serine,4TMS,isomer #1	C[Si](C)(C)OC[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1522.1	Standard non polar	33892256
D-Serine,4TMS,isomer #1	C[Si](C)(C)OC[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1440.7	Standard polar	33892256
D-Serine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H](N)C(=O)O	1460.8	Semi standard non polar	33892256
D-Serine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@H](N)CO	1384.7	Semi standard non polar	33892256
D-Serine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N[C@H](CO)C(=O)O	1525.0	Semi standard non polar	33892256
D-Serine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H](N)C(=O)O[Si](C)(C)C(C)(C)C	1697.4	Semi standard non polar	33892256
D-Serine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N[C@H](CO[Si](C)(C)C(C)(C)C)C(=O)O	1772.5	Semi standard non polar	33892256
D-Serine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N[C@H](CO)C(=O)O[Si](C)(C)C(C)(C)C	1729.7	Semi standard non polar	33892256
D-Serine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N([C@H](CO)C(=O)O)[Si](C)(C)C(C)(C)C	1906.9	Semi standard non polar	33892256
D-Serine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N[C@H](CO[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1997.4	Semi standard non polar	33892256
D-Serine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N[C@H](CO[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2018.7	Standard non polar	33892256
D-Serine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N[C@H](CO[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1887.9	Standard polar	33892256
D-Serine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2145.5	Semi standard non polar	33892256
D-Serine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2080.8	Standard non polar	33892256
D-Serine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1941.3	Standard polar	33892256
D-Serine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](CO)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2123.0	Semi standard non polar	33892256
D-Serine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](CO)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2056.5	Standard non polar	33892256
D-Serine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](CO)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1908.5	Standard polar	33892256
D-Serine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2386.5	Semi standard non polar	33892256
D-Serine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2312.5	Standard non polar	33892256
D-Serine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1970.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - D-Serine GC-MS (Non-derivatized) - 70eV, Positive	splash10-06sl-9000000000-033631650075b940e0e2	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Serine GC-MS (2 TMS) - 70eV, Positive	splash10-0089-9810000000-06fed7f6e260b107d95a	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Serine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Serine Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-03di-9000000000-d33888cff00d0ade0ffe	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Serine Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-03di-9000000000-f7e50afcb90768dce4a5	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Serine Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-0006-9000000000-043951ed5540cce44f4e	2012-07-25	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 10V, Positive-QTOF	splash10-08g0-9300000000-dab8446816db786db171	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 20V, Positive-QTOF	splash10-03dl-9000000000-1a5aef91299ef3583ca2	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 40V, Positive-QTOF	splash10-0006-9000000000-b6cfe52e68c644cacfd7	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 10V, Negative-QTOF	splash10-0udi-6900000000-ee98a5a83ffbd434740e	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 20V, Negative-QTOF	splash10-0uki-9200000000-fa8d04d6ce99a290d187	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 40V, Negative-QTOF	splash10-05fu-9000000000-001b18464fb313594dec	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 10V, Positive-QTOF	splash10-03di-9000000000-c00dff763ff1f56fda00	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 20V, Positive-QTOF	splash10-03di-9000000000-980e3923ad0861629a12	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 40V, Positive-QTOF	splash10-0006-9000000000-90338875078d415c5036	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 10V, Negative-QTOF	splash10-00di-9100000000-113290360f404e0abfe6	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 20V, Negative-QTOF	splash10-00di-9000000000-a5d4e47e8a548414bcb5	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Serine 40V, Negative-QTOF	splash10-0596-9000000000-45f597b943c27fee51e7	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Saliva
Urine

Tissue Locations

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

Pathways

Name	SMPDB/PathBank	KEGG
Transcription/Translation	SMP00019	Not Available
Glycine, serine and threonine metabolism	Not Available
Dimethylglycine Dehydrogenase Deficiency		Not Available
Dihydropyrimidine Dehydrogenase Deficiency (DHPD)		Not Available
Sarcosinemia		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	1.88 +/- 0.07 uM	Adult (>18 years old)	Both	Normal	25004141	details
Blood	Detected and Quantified	2.28 +/- 0.59 uM	Adult (>18 years old)	Both	Normal	12796220	details
Blood	Detected and Quantified	3.6 +/- 2.2 uM	Adult (>18 years old)	Male	Normal	16890503	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Urine	Detected and Quantified	0.0021 - 10.1 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	21389975	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	1.57 +/- 0.07 uM	Adult (>18 years old)	Both	Schizophrenia	25004141	details
Blood	Detected and Quantified	1.86 +/- 0.53 uM	Adult (>18 years old)	Both	Schizophrenia	12796220	details
Urine	Detected and Quantified	0.0041 - 0.0122 umol/mmol creatinine	Adult (>18 years old)	Both	ADPKD	21389975	details

Associated Disorders and Diseases

Disease References

Schizophrenia
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. [PubMed:12796220 ] 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. [PubMed:25004141 ]
Autosomal dominant polycystic kidney disease
Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, Deutschmann M, Immervoll AK, Boger CA, Banas B, Eckardt KU, Oefner PJ: Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int. 2011 Jun;79(11):1244-53. doi: 10.1038/ki.2011.30. Epub 2011 Mar 9. [PubMed:21389975 ]

Associated OMIM IDs

181500 (Schizophrenia)
601313 (Autosomal dominant polycystic kidney disease)

External Links

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

Food Biomarker Ontology

Not Available

VMH ID

SER_D

MarkerDB ID

MDB00000423

Good Scents ID

Not Available

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)

Download (PDF)

General References

Strauss JF 3rd, Kallen CB, Christenson LK, Watari H, Devoto L, Arakane F, Kiriakidou M, Sugawara T: The steroidogenic acute regulatory protein (StAR): a window into the complexities of intracellular cholesterol trafficking. Recent Prog Horm Res. 1999;54:369-94; discussion 394-5. [PubMed:10548884 ]
Shafqat S, Tamarappoo BK, Kilberg MS, Puranam RS, McNamara JO, Guadano-Ferraz A, Fremeau RT Jr: Cloning and expression of a novel Na(+)-dependent neutral amino acid transporter structurally related to mammalian Na+/glutamate cotransporters. J Biol Chem. 1993 Jul 25;268(21):15351-5. [PubMed:8340364 ]
Jones CM, Smith M, Henderson MJ: Reference data for cerebrospinal fluid and the utility of amino acid measurement for the diagnosis of inborn errors of metabolism. Ann Clin Biochem. 2006 Jan;43(Pt 1):63-6. [PubMed:16390611 ]
Nanda N, Bao M, Lin H, Clauser K, Komuves L, Quertermous T, Conley PB, Phillips DR, Hart MJ: Platelet endothelial aggregation receptor 1 (PEAR1), a novel epidermal growth factor repeat-containing transmembrane receptor, participates in platelet contact-induced activation. J Biol Chem. 2005 Jul 1;280(26):24680-9. Epub 2005 Apr 25. [PubMed:15851471 ]
Amberger VR, Hensel T, Ogata N, Schwab ME: Spreading and migration of human glioma and rat C6 cells on central nervous system myelin in vitro is correlated with tumor malignancy and involves a metalloproteolytic activity. Cancer Res. 1998 Jan 1;58(1):149-58. [PubMed:9426071 ]
Boehning D, Snyder SH: Novel neural modulators. Annu Rev Neurosci. 2003;26:105-31. [PubMed:14527267 ]
Hansson L, Stromqvist M, Backman A, Wallbrandt P, Carlstein A, Egelrud T: Cloning, expression, and characterization of stratum corneum chymotryptic enzyme. A skin-specific human serine proteinase. J Biol Chem. 1994 Jul 29;269(30):19420-6. [PubMed:8034709 ]
Deshpande RV, Goust JM, Hogan EL, Banik NL: Calpain secreted by activated human lymphoid cells degrades myelin. J Neurosci Res. 1995 Oct 1;42(2):259-65. [PubMed:8568927 ]
Metzner L, Kottra G, Neubert K, Daniel H, Brandsch M: Serotonin, L-tryptophan, and tryptamine are effective inhibitors of the amino acid transport system PAT1. FASEB J. 2005 Sep;19(11):1468-73. [PubMed:16126914 ]
Nagata Y, Higashi M, Ishii Y, Sano H, Tanigawa M, Nagata K, Noguchi K, Urade M: The presence of high concentrations of free D-amino acids in human saliva. Life Sci. 2006 Mar 6;78(15):1677-81. Epub 2006 Feb 9. [PubMed:16480744 ]
Nuesch JP, Corbau R, Tattersall P, Rommelaere J: Biochemical activities of minute virus of mice nonstructural protein NS1 are modulated In vitro by the phosphorylation state of the polypeptide. J Virol. 1998 Oct;72(10):8002-12. [PubMed:9733839 ]
Tsuei DJ, Hsu HC, Lee PH, Jeng YM, Pu YS, Chen CN, Lee YC, Chou WC, Chang CJ, Ni YH, Chang MH: RBMY, a male germ cell-specific RNA-binding protein, activated in human liver cancers and transforms rodent fibroblasts. Oncogene. 2004 Jul 29;23(34):5815-22. [PubMed:15184870 ]
Yu LY, Jokitalo E, Sun YF, Mehlen P, Lindholm D, Saarma M, Arumae U: GDNF-deprived sympathetic neurons die via a novel nonmitochondrial pathway. J Cell Biol. 2003 Dec 8;163(5):987-97. Epub 2003 Dec 1. [PubMed:14657232 ]
Franzke CW, Baici A, Bartels J, Christophers E, Wiedow O: Antileukoprotease inhibits stratum corneum chymotryptic enzyme. Evidence for a regulative function in desquamation. J Biol Chem. 1996 Sep 6;271(36):21886-90. [PubMed:8702990 ]
Hooper JD, Nicol DL, Dickinson JL, Eyre HJ, Scarman AL, Normyle JF, Stuttgen MA, Douglas ML, Loveland KA, Sutherland GR, Antalis TM: Testisin, a new human serine proteinase expressed by premeiotic testicular germ cells and lost in testicular germ cell tumors. Cancer Res. 1999 Jul 1;59(13):3199-205. [PubMed:10397266 ]
Ishida-Takahashi R, Rosario F, Gong Y, Kopp K, Stancheva Z, Chen X, Feener EP, Myers MG Jr: Phosphorylation of Jak2 on Ser(523) inhibits Jak2-dependent leptin receptor signaling. Mol Cell Biol. 2006 Jun;26(11):4063-73. [PubMed:16705160 ]
Farhana L, Dawson MI, Huang Y, Zhang Y, Rishi AK, Reddy KB, Freeman RS, Fontana JA: Apoptosis signaling by the novel compound 3-Cl-AHPC involves increased EGFR proteolysis and accompanying decreased phosphatidylinositol 3-kinase and AKT kinase activities. Oncogene. 2004 Mar 11;23(10):1874-84. [PubMed:14981538 ]
Taniguchi A, Kataoka K, Kono T, Oseko F, Okuda H, Nagata I, Imura H: Parathyroid hormone-induced lipolysis in human adipose tissue. J Lipid Res. 1987 May;28(5):490-4. [PubMed:3598394 ]
Dietze-Schroeder D, Sell H, Uhlig M, Koenen M, Eckel J: Autocrine action of adiponectin on human fat cells prevents the release of insulin resistance-inducing factors. Diabetes. 2005 Jul;54(7):2003-11. [PubMed:15983200 ]
Stewart LV, Song K, Hsing AY, Danielpour D: Regulation of trespin expression by modulators of cell growth, differentiation, and apoptosis in prostatic epithelial cells. Exp Cell Res. 2003 Apr 1;284(2):303-15. [PubMed:12651162 ]
Pfundt R, van Ruissen F, van Vlijmen-Willems IM, Alkemade HA, Zeeuwen PL, Jap PH, Dijkman H, Fransen J, Croes H, van Erp PE, Schalkwijk J: Constitutive and inducible expression of SKALP/elafin provides anti-elastase defense in human epithelia. J Clin Invest. 1996 Sep 15;98(6):1389-99. [PubMed:8823304 ]
Kim JK, Fillmore JJ, Sunshine MJ, Albrecht B, Higashimori T, Kim DW, Liu ZX, Soos TJ, Cline GW, O'Brien WR, Littman DR, Shulman GI: PKC-theta knockout mice are protected from fat-induced insulin resistance. J Clin Invest. 2004 Sep;114(6):823-7. [PubMed:15372106 ]
Olive PL, Banath JP, Sinnott LT: Phosphorylated histone H2AX in spheroids, tumors, and tissues of mice exposed to etoposide and 3-amino-1,2,4-benzotriazine-1,3-dioxide. Cancer Res. 2004 Aug 1;64(15):5363-9. [PubMed:15289343 ]
Hinek A, Smith AC, Cutiongco EM, Callahan JW, Gripp KW, Weksberg R: Decreased elastin deposition and high proliferation of fibroblasts from Costello syndrome are related to functional deficiency in the 67-kD elastin-binding protein. Am J Hum Genet. 2000 Mar;66(3):859-72. [PubMed:10712202 ]
Lavker RM, Risse B, Brown H, Ginsburg D, Pearson J, Baker MS, Jensen PJ: Localization of plasminogen activator inhibitor type 2 (PAI-2) in hair and nail: implications for terminal differentiation. J Invest Dermatol. 1998 Jun;110(6):917-22. [PubMed:9620299 ]
Paju A, Bjartell A, Zhang WM, Nordling S, Borgstrom A, Hansson J, Stenman UH: Expression and characterization of trypsinogen produced in the human male genital tract. Am J Pathol. 2000 Dec;157(6):2011-21. [PubMed:11106574 ]
Schultess J, Danielewski O, Smolenski AP: Rap1GAP2 is a new GTPase-activating protein of Rap1 expressed in human platelets. Blood. 2005 Apr 15;105(8):3185-92. Epub 2005 Jan 4. [PubMed:15632203 ]
Alvarez JV, Greulich H, Sellers WR, Meyerson M, Frank DA: Signal transducer and activator of transcription 3 is required for the oncogenic effects of non-small-cell lung cancer-associated mutations of the epidermal growth factor receptor. Cancer Res. 2006 Mar 15;66(6):3162-8. [PubMed:16540667 ]
Hayes GM, Carrigan PE, Beck AM, Miller LJ: Targeting the RNA splicing machinery as a novel treatment strategy for pancreatic carcinoma. Cancer Res. 2006 Apr 1;66(7):3819-27. [PubMed:16585209 ]
Roesch PL, Redford P, Batchelet S, Moritz RL, Pellett S, Haugen BJ, Blattner FR, Welch RA: Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of the murine urinary tract. Mol Microbiol. 2003 Jul;49(1):55-67. [PubMed:12823810 ]
Wyatt AW, Hussain A, Amann K, Klingel K, Kandolf R, Artunc F, Grahammer F, Huang DY, Vallon V, Kuhl D, Lang F: DOCA-induced phosphorylation of glycogen synthase kinase 3beta. Cell Physiol Biochem. 2006;17(3-4):137-44. Epub 2006 Mar 14. [PubMed:16543730 ]
Khamzina L, Veilleux A, Bergeron S, Marette A: Increased activation of the mammalian target of rapamycin pathway in liver and skeletal muscle of obese rats: possible involvement in obesity-linked insulin resistance. Endocrinology. 2005 Mar;146(3):1473-81. Epub 2004 Dec 16. [PubMed:15604215 ]
Morino K, Petersen KF, Dufour S, Befroy D, Frattini J, Shatzkes N, Neschen S, White MF, Bilz S, Sono S, Pypaert M, Shulman GI: Reduced mitochondrial density and increased IRS-1 serine phosphorylation in muscle of insulin-resistant offspring of type 2 diabetic parents. J Clin Invest. 2005 Dec;115(12):3587-93. Epub 2005 Nov 10. [PubMed:16284649 ]
Zhu L, Wigle D, Hinek A, Kobayashi J, Ye C, Zuker M, Dodo H, Keeley FW, Rabinovitch M: The endogenous vascular elastase that governs development and progression of monocrotaline-induced pulmonary hypertension in rats is a novel enzyme related to the serine proteinase adipsin. J Clin Invest. 1994 Sep;94(3):1163-71. [PubMed:8083356 ]

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. 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

Enzyme Details

3. 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

Reactions

L-Serine → D-Serine	details
D-Serine → Pyruvic acid + Ammonia	details

Showing metabocard for D-Serine (HMDB0003406)

MOL for HMDB0003406 (D-Serine)

3D MOL for HMDB0003406 (D-Serine)

3D SDF for HMDB0003406 (D-Serine)

3D-SDF for HMDB0003406 (D-Serine)

PDB for HMDB0003406 (D-Serine)

3D PDB for HMDB0003406 (D-Serine)

SMILES for HMDB0003406 (D-Serine)

INCHI for HMDB0003406 (D-Serine)

Structure for HMDB0003406 (D-Serine)

3D Structure for HMDB0003406 (D-Serine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions