General Information of MET (ID: META00519)
Name D-Serine
Synonyms   Click to Show/Hide Synonyms of This Metabolite
(2R)-2-Amino-3-hydroxypropanoate; (2R)-2-Amino-3-hydroxypropanoic acid; (R)-2-Amino-3-hydroxy-propionate; (R)-2-Amino-3-hydroxy-propionic acid; (R)-2-Amino-3-hydroxypropanoate; (R)-2-Amino-3-hydroxypropanoic acid; D-Serin; DL-Serine; DSN; Serine D-form
Source Endogenous;Escherichia Coli Metabolite;Yeast Metabolite;Food;Drug;Microbial
Structure Type   Amino acids, peptides, and analogues  (Click to Show/Hide the Complete Structure Type Hierarchy)
Organic acids and derivatives
Carboxylic acids and derivatives
Amino acids, peptides, and analogues
PubChem CID
71077
HMDB ID
HMDB0003406
Formula
C3H7NO3
Structure
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3D MOL 2D MOL
  Click to Show/Hide the Molecular/Functional Data (External Links/Property/Function) of This Metabolite
KEGG ID
C00740
DrugBank ID
DB03929
ChEBI ID
16523
FooDB ID
FDB023164
ChemSpider ID
64231
METLIN ID
6920
Physicochemical Properties Molecular Weight 105.09 Topological Polar Surface Area 83.6
XlogP -3.1 Complexity 72.6
Heavy Atom Count 7 Rotatable Bond Count 2
Hydrogen Bond Donor Count 3 Hydrogen Bond Acceptor Count 4
Function
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.
Regulatory Network
Full List of Protein(s) Regulating This Metabolite
      Dicarboxylate/amino acid:cation symporter (DAACS)
            Neutral amino acid transporter A (SLC1A4) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [1]
                      Introduced Variation Knockout of SLC1A4
                      Induced Change D-Serine concentration: decrease (FC = 0.10-0.20)
                      Summary Introduced Variation         Induced Change 
                      Disease Status Healthy individual
                      Details It is reported that knockout of SLC1A4 leads to the decrease of D-Serine levels compared with control group.
      Hydrolases (EC 3)
            Glycerophosphodiester phosphodiesterase 1 (GDE1) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [2]
                      Introduced Variation Knockout of Gde1
                      Induced Change D-Serine concentration: decrease (FC= 1.6)
                      Summary Introduced Variation         Induced Change 
                      Disease Status Healthy individual
                      Details It is reported that knockout of Gde1 leads to the decrease of D-Serine levels compared with control group.
      Pore-forming PNC peptide (PNC)
            Cellular tumor antigen p53 (TP53) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [3]
                      Introduced Variation Knockout of TP53
                      Induced Change D-Serine concentration: decrease (Log2 FC=0.75)
                      Summary Introduced Variation         Induced Change 
                      Disease Status Colon cancer [ICD-11: 2B90]
                      Details It is reported that knockout of TP53 leads to the decrease of D-Serine levels compared with control group.
References
1 ASCT1 (Slc1a4) transporter is a physiologic regulator of brain d-serine and neurodevelopment. Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9628-9633.
2 The glycerophospho metabolome and its influence on amino acid homeostasis revealed by brain metabolomics of GDE1(-/-) mice. Chem Biol. 2010 Aug 27;17(8):831-40.
3 Integrative omics analysis of p53-dependent regulation of metabolism. FEBS Lett. 2018 Feb;592(3):380-393.

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