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Showing metabocard for DL-O-Phosphoserine (HMDB0001721)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-20 22:13:21 UTC
Update Date2021-09-14 15:20:03 UTC
HMDB IDHMDB0001721
Secondary Accession Numbers
  • HMDB01721
Metabolite Identification
Common NameDL-O-Phosphoserine
DescriptionDL-O-Phosphoserine, also known as DL-O-phosphorylserine or DL-O-serine phosphate, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Serine proteases are a common type of protease. DL-O-Phosphoserine exists in all living species, ranging from bacteria to humans. Serine is one of three amino acid residues that are commonly phosphorylated by kinases during cell signalling in eukaryotes.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001721 (DL-O-Phosphoserine)

  Mrv1652309042000252D          

 11 10  0  0  0  0            999 V2000
    9.9354   -6.7252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6459   -6.3059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3563   -6.7252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0668   -6.3059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7889   -6.7135    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0668   -5.4790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3563   -7.5521    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2135   -6.3176    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.4914   -5.9099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8058   -7.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6210   -5.5955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  8  1  1  0  0  0  0
  3  2  1  0  0  0  0
  3  7  1  0  0  0  0
  4  3  1  0  0  0  0
  6  4  2  0  0  0  0
  5  4  1  0  0  0  0
  9  8  2  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0001721 (DL-O-Phosphoserine)

HMDB0001721
     RDKit          3D
DL-O-Phosphoserine
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.3441   -1.8756    0.8434 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4323   -0.8049   -0.0864 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0178   -0.3913   -0.4631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6908    0.0250    0.6646 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2429    0.4737    0.2194 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.5642   -0.1987   -1.0880 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3956   -0.0823    1.3486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4136    2.1588    0.1029 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2031    0.3574    0.4397 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6857    0.3009    1.5966 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4065    1.4980   -0.3011 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5380   -2.8140    0.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6881   -1.6790    1.7959 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9509   -1.1319   -1.0057 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0492    0.4262   -1.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4772   -1.3085   -0.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2861    0.2196    0.9820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8812    2.4523   -0.6711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6359    2.3741    0.1439 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  0
  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 HMDB0001721 (DL-O-Phosphoserine)

  Mrv1652309042000252D          

 11 10  0  0  0  0            999 V2000
    9.9354   -6.7252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6459   -6.3059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3563   -6.7252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0668   -6.3059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7889   -6.7135    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0668   -5.4790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3563   -7.5521    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2135   -6.3176    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.4914   -5.9099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8058   -7.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6210   -5.5955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  8  1  1  0  0  0  0
  3  2  1  0  0  0  0
  3  7  1  0  0  0  0
  4  3  1  0  0  0  0
  6  4  2  0  0  0  0
  5  4  1  0  0  0  0
  9  8  2  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001721

> <DATABASE_NAME>
hmdb

> <SMILES>
NC(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)

> <INCHI_KEY>
BZQFBWGGLXLEPQ-UHFFFAOYSA-N

> <FORMULA>
C3H8NO6P

> <MOLECULAR_WEIGHT>
185.0725

> <EXACT_MASS>
185.008923505

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.008769274759121

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
2.0667419682108834

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1985006020847053

> <JCHEM_PKA_STRONGEST_BASIC>
9.39423622748354

> <JCHEM_POLAR_SURFACE_AREA>
130.08

> <JCHEM_REFRACTIVITY>
32.913900000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.99e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
P-serine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001721 (DL-O-Phosphoserine)

HMDB0001721
     RDKit          3D
DL-O-Phosphoserine
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.3441   -1.8756    0.8434 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4323   -0.8049   -0.0864 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0178   -0.3913   -0.4631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6908    0.0250    0.6646 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2429    0.4737    0.2194 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.5642   -0.1987   -1.0880 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3956   -0.0823    1.3486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4136    2.1588    0.1029 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2031    0.3574    0.4397 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6857    0.3009    1.5966 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4065    1.4980   -0.3011 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5380   -2.8140    0.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6881   -1.6790    1.7959 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9509   -1.1319   -1.0057 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0492    0.4262   -1.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4772   -1.3085   -0.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2861    0.2196    0.9820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8812    2.4523   -0.6711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6359    2.3741    0.1439 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  0
  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 HMDB0001721 (DL-O-Phosphoserine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0      18.546 -12.554   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      19.872 -11.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.198 -12.554   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      22.525 -11.771   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      23.873 -12.532   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      22.525 -10.227   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      21.198 -14.097   0.000  0.00  0.00           N+0
HETATM    8  P   UNK     0      17.199 -11.793   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0      15.851 -11.032   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      16.437 -13.141   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.959 -10.445   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    7    4                                                  
CONECT    4    3    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
CONECT    8    1    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0001721 (DL-O-Phosphoserine)

COMPND    HMDB0001721
HETATM    1  N1  UNL     1       1.344  -1.876   0.843  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.432  -0.805  -0.086  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.018  -0.391  -0.463  1.00  0.00           C  
HETATM    4  O1  UNL     1      -0.691   0.025   0.665  1.00  0.00           O  
HETATM    5  P1  UNL     1      -2.243   0.474   0.219  1.00  0.00           P  
HETATM    6  O2  UNL     1      -2.564  -0.199  -1.088  1.00  0.00           O  
HETATM    7  O3  UNL     1      -3.396  -0.082   1.349  1.00  0.00           O  
HETATM    8  O4  UNL     1      -2.414   2.159   0.103  1.00  0.00           O  
HETATM    9  C3  UNL     1       2.203   0.357   0.440  1.00  0.00           C  
HETATM   10  O5  UNL     1       2.686   0.301   1.597  1.00  0.00           O  
HETATM   11  O6  UNL     1       2.407   1.498  -0.301  1.00  0.00           O  
HETATM   12  H1  UNL     1       1.538  -2.814   0.478  1.00  0.00           H  
HETATM   13  H2  UNL     1       1.688  -1.679   1.796  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.951  -1.132  -1.006  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.049   0.426  -1.179  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.477  -1.308  -0.844  1.00  0.00           H  
HETATM   17  H6  UNL     1      -4.286   0.220   0.982  1.00  0.00           H  
HETATM   18  H7  UNL     1      -1.881   2.452  -0.671  1.00  0.00           H  
HETATM   19  H8  UNL     1       2.636   2.374   0.144  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 HMDB0001721 (DL-O-Phosphoserine)

NC(COP(O)(O)=O)C(O)=O
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INCHI for HMDB0001721 (DL-O-Phosphoserine)

InChI=1S/C3H8NO6P/c4-2(3(5)6)1-10-11(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC3H8NO6P
Average Molecular Weight185.0725
Monoisotopic Molecular Weight185.008923505
IUPAC Name2-amino-3-(phosphonooxy)propanoic acid
Traditional NameP-serine
CAS Registry Number17885-08-4
SMILES
NC(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)
InChI KeyBZQFBWGGLXLEPQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Phosphoethanolamine
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Primary amine
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point228 °CNot 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 Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Epidermis
  • Testis
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
UrineDetected and Quantified1.05 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.33 +/- 0.001 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022700
KNApSAcK IDNot Available
Chemspider ID104
KEGG Compound IDC01005
BioCyc IDNot Available
BiGG ID36594
Wikipedia LinkPhosphoserine
METLIN ID6338
PubChem Compound106
PDB IDNot Available
ChEBI ID37712
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceLacombe J M; Andriamanampisoa F; Pavia A A Solid-phase synthesis of peptides containing phosphoserine using phosphate tert.-butyl protecting group. International journal of peptide and protein research (1990), 36(3), 275-80.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Phosphoserine aminotransferase
General function:
Involved in metabolic process
Specific function:
Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine (By similarity).
Gene Name:
PSAT1
Uniprot ID:
Q9Y617
Molecular weight:
35188.305
Enzyme Details
2. 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