Showing metabocard for D-Serine (MMDBc0000241)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:41:01 UTC
Update Date2022-08-31 00:16:00 UTC
Metabolite IDMMDBc0000241
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055c79c505348>


  Mrv1652308122017382D          

  7  6  0  0  1  0            999 V2000
    0.0000   -1.0313    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4291   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4291   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x000055c79c505348>

HMDB0003406
     RDKit          3D
D-Serine
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.5556    0.5520   -1.3533 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.4442   -0.0588 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2250   -0.5078   -0.1469 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8061   -0.6059    1.1091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9017   -0.0243    0.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5346   -0.1733    2.1609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2259   -0.3122    0.6675 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2415    1.3167   -1.4432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8403   -0.3497   -1.7732 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4185    1.4530    0.2230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9983   -0.1181   -0.8382 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8557   -1.5111   -0.4251 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4809    0.1056    1.1906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5368   -0.2690   -0.2877 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
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3D SDF for #<Metabolite:0x000055c79c505348>


  Mrv1652308122017382D          

  7  6  0  0  1  0            999 V2000
    0.0000   -1.0313    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4291   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4291   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000241

> <DATABASE_NAME>
MIME

> <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

> <FORMULA>
C3H7NO3

> <MOLECULAR_WEIGHT>
105.0926

> <EXACT_MASS>
105.042593095

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
9.387821307652931

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-hydroxypropanoic acid

> <ALOGPS_LOGP>
-3.42

> <JCHEM_LOGP>
-3.8877352328917727

> <ALOGPS_LOGS>
0.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.166073878847005

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.033990015469951

> <JCHEM_PKA_STRONGEST_BASIC>
8.931303956589883

> <JCHEM_POLAR_SURFACE_AREA>
83.55000000000001

> <JCHEM_REFRACTIVITY>
22.041000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-serine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055c79c505348>

HMDB0003406
     RDKit          3D
D-Serine
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.5556    0.5520   -1.3533 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.4442   -0.0588 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2250   -0.5078   -0.1469 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8061   -0.6059    1.1091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9017   -0.0243    0.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5346   -0.1733    2.1609 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2259   -0.3122    0.6675 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2415    1.3167   -1.4432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8403   -0.3497   -1.7732 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4185    1.4530    0.2230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9983   -0.1181   -0.8382 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8557   -1.5111   -0.4251 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4809    0.1056    1.1906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5368   -0.2690   -0.2877 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
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PDB for #<Metabolite:0x000055c79c505348>

HEADER    PROTEIN                                 12-AUG-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-AUG-20         0                                  
HETATM    1  N   UNK     0       0.000  -1.925   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.385   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.668  -0.385   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334   0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.668  -0.385   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -1.334   1.925   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for #<Metabolite:0x000055c79c505348>

COMPND    HMDB0003406
HETATM    1  N1  UNL     1      -0.556   0.552  -1.353  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.052   0.444  -0.059  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.225  -0.508  -0.147  1.00  0.00           C  
HETATM    4  O1  UNL     1       1.806  -0.606   1.109  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.902  -0.024   0.975  1.00  0.00           C  
HETATM    6  O2  UNL     1      -0.535  -0.173   2.161  1.00  0.00           O  
HETATM    7  O3  UNL     1      -2.226  -0.312   0.668  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.241   1.317  -1.443  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.840  -0.350  -1.773  1.00  0.00           H  
HETATM   10  H3  UNL     1       0.419   1.453   0.223  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.998  -0.118  -0.838  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.856  -1.511  -0.425  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.481   0.106   1.191  1.00  0.00           H  
HETATM   14  H7  UNL     1      -2.537  -0.269  -0.288  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3    5   10
CONECT    3    4   11   12
CONECT    4   13
CONECT    5    6    6    7
CONECT    7   14
END
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SMILES for #<Metabolite:0x000055c79c505348>

N[C@H](CO)C(O)=O
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INCHI for #<Metabolite:0x000055c79c505348>

InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
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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
Molecular FormulaC3H7NO3
Average Mass105.0926
Monoisotopic Mass105.042593095
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 KeyMTCFGRXMJLQNBG-UWTATZPHSA-N