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Showing metabocard for 3-phospho-L-serine (HMDB0304154)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:37:26 UTC
Update Date2021-09-24 07:37:26 UTC
HMDB IDHMDB0304154
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-phospho-L-serine
DescriptionO-phospho-d-serine, also known as (2r)-2-amino-3-(phosphonooxy)propanoic acid, is a member of the class of compounds known as D-alpha-amino acids. D-alpha-amino acids are alpha amino acids which have the D-configuration of the alpha-carbon atom. O-phospho-d-serine is soluble (in water) and a moderately acidic compound (based on its pKa). O-phospho-d-serine can be found in a number of food items such as mugwort, rambutan, common persimmon, and ostrich fern, which makes O-phospho-d-serine a potential biomarker for the consumption of these food products. O-phospho-d-serine may be a unique E.coli metabolite.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304154 (3-phospho-L-serine)

  Mrv0541 08131209372D          

 12 11  0  0  0  0            999 V2000
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  2  4  1  6  0  0  0
  5  3  2  0  0  0  0
  6  3  1  0  0  0  0
 10  1  1  0  0  0  0
 11  7  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  2  0  0  0  0
 11 10  1  0  0  0  0
  2 12  1  6  0  0  0
M  END
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3D MOL for HMDB0304154 (3-phospho-L-serine)

HMDB0304154
     RDKit          3D
3-phospho-L-serine
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.0284   -1.0907   -0.7711 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5567    0.2398   -0.5822 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0397    0.2078   -0.6607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4840   -0.6162    0.3164 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1691   -0.5942    0.1582 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.6597   -1.8033   -0.6166 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6423    0.7861   -0.6965 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8928   -0.6101    1.6875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0239    0.7986    0.7045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7414    0.0715    1.4352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7116    2.0733    1.1393 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9627   -1.6956    0.0646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9299   -1.1709   -1.2782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9381    0.8840   -1.4108 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3549    1.2578   -0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3040   -0.1202   -1.6620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4664    0.6451   -1.2021 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0730   -1.5265    1.9771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1137    2.2637    1.9392 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  5  8  1  0
  2  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  3 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
 11 19  1  0
M  END
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3D SDF for HMDB0304154 (3-phospho-L-serine)

  Mrv0541 08131209372D          

 12 11  0  0  0  0            999 V2000
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  2  4  1  6  0  0  0
  5  3  2  0  0  0  0
  6  3  1  0  0  0  0
 10  1  1  0  0  0  0
 11  7  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  2  0  0  0  0
 11 10  1  0  0  0  0
  2 12  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0304154

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](N)(COP(O)(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H8NO6P/c4-2(3(5)6)1-10-11(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1

> <INCHI_KEY>
BZQFBWGGLXLEPQ-UWTATZPHSA-N

> <FORMULA>
C3H8NO6P

> <MOLECULAR_WEIGHT>
185.0725

> <EXACT_MASS>
185.008923505

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
14.055033276744453

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-(phosphonooxy)propanoic acid

> <ALOGPS_LOGP>
-2.32

> <JCHEM_LOGP>
-3.180275047030002

> <ALOGPS_LOGS>
-0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.0667419682108825

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1985006020847058

> <JCHEM_PKA_STRONGEST_BASIC>
9.39423622748354

> <JCHEM_POLAR_SURFACE_AREA>
130.08

> <JCHEM_REFRACTIVITY>
32.9139

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.99e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
O-phospho-D-serine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304154 (3-phospho-L-serine)

HMDB0304154
     RDKit          3D
3-phospho-L-serine
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.0284   -1.0907   -0.7711 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5567    0.2398   -0.5822 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0397    0.2078   -0.6607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4840   -0.6162    0.3164 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1691   -0.5942    0.1582 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.6597   -1.8033   -0.6166 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6423    0.7861   -0.6965 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8928   -0.6101    1.6875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0239    0.7986    0.7045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7414    0.0715    1.4352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7116    2.0733    1.1393 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9627   -1.6956    0.0646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9299   -1.1709   -1.2782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9381    0.8840   -1.4108 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3549    1.2578   -0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3040   -0.1202   -1.6620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4664    0.6451   -1.2021 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0730   -1.5265    1.9771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1137    2.2637    1.9392 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  5  8  1  0
  2  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  3 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
 11 19  1  0
M  END
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PDB for HMDB0304154 (3-phospho-L-serine)

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2   10                                                       
CONECT    2    1    3    4   12                                             
CONECT    3    2    5    6                                                  
CONECT    4    2                                                            
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7   11                                                            
CONECT    8   11                                                            
CONECT    9   11                                                            
CONECT   10    1   11                                                       
CONECT   11    7    8    9   10                                             
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for HMDB0304154 (3-phospho-L-serine)

COMPND    HMDB0304154
HETATM    1  N1  UNL     1      -2.028  -1.091  -0.771  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.557   0.240  -0.582  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.040   0.208  -0.661  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.484  -0.616   0.316  1.00  0.00           O  
HETATM    5  P1  UNL     1       2.169  -0.594   0.158  1.00  0.00           P  
HETATM    6  O2  UNL     1       2.660  -1.803  -0.617  1.00  0.00           O  
HETATM    7  O3  UNL     1       2.642   0.786  -0.696  1.00  0.00           O  
HETATM    8  O4  UNL     1       2.893  -0.610   1.688  1.00  0.00           O  
HETATM    9  C3  UNL     1      -2.024   0.799   0.705  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.741   0.072   1.435  1.00  0.00           O  
HETATM   11  O6  UNL     1      -1.712   2.073   1.139  1.00  0.00           O  
HETATM   12  H1  UNL     1      -1.963  -1.696   0.065  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.930  -1.171  -1.278  1.00  0.00           H  
HETATM   14  H3  UNL     1      -1.938   0.884  -1.411  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.355   1.258  -0.542  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.304  -0.120  -1.662  1.00  0.00           H  
HETATM   17  H6  UNL     1       3.466   0.645  -1.202  1.00  0.00           H  
HETATM   18  H7  UNL     1       3.073  -1.527   1.977  1.00  0.00           H  
HETATM   19  H8  UNL     1      -1.114   2.264   1.939  1.00  0.00           H  
CONECT    1    2   12   13
CONECT    2    3    9   14
CONECT    3    4   15   16
CONECT    4    5
CONECT    5    6    6    7    8
CONECT    7   17
CONECT    8   18
CONECT    9   10   10   11
CONECT   11   19
END
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SMILES for HMDB0304154 (3-phospho-L-serine)

[H][C@@](N)(COP(O)(O)=O)C(O)=O
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INCHI for HMDB0304154 (3-phospho-L-serine)

InChI=1S/C3H8NO6P/c4-2(3(5)6)1-10-11(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(2R)-2-Amino-3-(phosphonooxy)propanoic acidChEBI
D-O-PhosphoserineChEBI
(2R)-2-Amino-3-(phosphonooxy)propanoateGenerator
Chemical FormulaC3H8NO6P
Average Molecular Weight185.0725
Monoisotopic Molecular Weight185.008923505
IUPAC Name(2R)-2-amino-3-(phosphonooxy)propanoic acid
Traditional NameO-phospho-D-serine
CAS Registry NumberNot Available
SMILES
[H][C@@](N)(COP(O)(O)=O)C(O)=O
InChI Identifier
InChI=1S/C3H8NO6P/c4-2(3(5)6)1-10-11(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
InChI KeyBZQFBWGGLXLEPQ-UWTATZPHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentD-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Phosphoethanolamine
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Primary amine
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Amine
  • Primary aliphatic amine
  • Carbonyl group
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030462
KNApSAcK IDNot Available
Chemspider ID388807
KEGG Compound IDC02532
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID37713
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available