Showing NP-Card for D-Serine (NP0000286)

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Record Information
Version2.0
Created at2006-08-12 20:15:26 UTC
Updated at2021-08-19 23:58:00 UTC
NP-MRD IDNP0000286
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000286 (D-Serine)

  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 NP0000286 (D-Serine)

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 NP0000286 (D-Serine)

  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>
NP0000286

> <DATABASE_NAME>
NP-MRD

> <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 NP0000286 (D-Serine)

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 NP0000286 (D-Serine)

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 NP0000286 (D-Serine)

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 NP0000286 (D-Serine)

N[C@H](CO)C(O)=O
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INCHI for NP0000286 (D-Serine)

InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
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View in JSmol
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 Mass105.0926 Da
Monoisotopic Mass105.04259 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Streptomyces lasaliensisKNApSAcK Database
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point229 °CNot Available
Boiling Point394.82 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility364 mg/mL at 20 °CNot Available
LogP-1.490 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility480 g/LALOGPS
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
HMDB IDHMDB0003406
DrugBank IDDB03929
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023164
KNApSAcK IDC00052032
Chemspider ID64231
KEGG Compound IDC00740
BioCyc IDD-SERINE
BiGG ID35846
Wikipedia LinkSerine
METLIN ID6920
PubChem Compound71077
PDB IDNot Available
ChEBI ID16523
Good Scents IDrw1234171
References
General References
  1. Boehning D, Snyder SH: Novel neural modulators. Annu Rev Neurosci. 2003;26:105-31. [PubMed:14527267 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]