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Showing NP-Card for serin (NP0236267)

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Record Information
Version2.0
Created at2022-09-06 19:07:10 UTC
Updated at2022-09-06 19:07:10 UTC
NP-MRD IDNP0236267
Secondary Accession NumbersNone
Natural Product Identification
Common Nameserin
DescriptionL-Serine, also known as 3-hydroxyalanine or serin, 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. Thus, L-serine is considered to be a fatty acid lipid molecule. An alpha-amino acid that is alanine substituted at position 3 by a hydroxy group. L-Serine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Within humans, L-serine participates in a number of enzymatic reactions. In particular, tetrahydrofolic acid and L-serine can be biosynthesized from 5,10-methylene-THF and glycine; which is catalyzed by the enzyme serine hydroxymethyltransferase, mitochondrial. In addition, pyruvic acid and L-serine can be converted into hydroxypyruvic acid and L-alanine through the action of the enzyme serine--pyruvate aminotransferase. In humans, L-serine is involved in the metabolic disorder called sarcosinemia. Outside of the human body, L-Serine is found, on average, in the highest concentration within a few different foods, such as caseins, red bell peppers, and milk (cow) and in a lower concentration in garden onions, celery leaves, and ginkgo nuts. L-Serine has also been detected, but not quantified in, several different foods, such as blue whitings, norway pouts, pomes, pepper (c. Pubescens), and rocket salad (ssp.). serin is found in Abutilon indicum, Agave americana, Allium rotundum, Antirrhinum majus, Arabidopsis thaliana, Bombyx mori, Castanea sativa, Chlamydomonas reinhardtii, Claviceps purpurea, Colchicum trigynum, Glycine max, Lates calcarifer, Lemna aequinoctialis, Litoria verreauxii, Lunaria annua, Medicago sativa, Mycoplasma gallisepticum, Onobrychis kachetica, Panax ginseng, Paris fargesii, Populus tremula, Puccinia graminis, Salmonella enterica, Scolopendra subspinipes, Solanum lycopersicum, Stellaria media and Viscum album. This could make L-serine a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0236267 (serin)


  Mrv1652305221920222D          

  7  6  0  0  0  0            999 V2000
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
M  END
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3D MOL for NP0236267 (serin)

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3D SDF for NP0236267 (serin)

  Mrv1652305221920222D          

  7  6  0  0  0  0            999 V2000
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0236267

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)

> <INCHI_KEY>
MTCFGRXMJLQNBG-UHFFFAOYSA-N

> <FORMULA>
C3H7NO3

> <MOLECULAR_WEIGHT>
105.0926

> <EXACT_MASS>
105.042593095

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
9.447823385108755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
83.55

> <JCHEM_REFRACTIVITY>
22.041

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
serin

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0236267 (serin)
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PDB for NP0236267 (serin)
HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       3.850   1.334   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.310  -1.334   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
CONECT    1    2    5                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2    6    7                                                  
CONECT    4    2                                                            
CONECT    5    1                                                            
CONECT    6    3                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END

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3D PDB for NP0236267 (serin)
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SMILES for NP0236267 (serin)
NC(CO)C(O)=O
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INCHI for NP0236267 (serin)
InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)
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Synonyms
ValueSource
2-Amino-3-hydroxypropanoic acidChEBI
2-Amino-3-hydroxypropionic acidChEBI
3-HydroxyalanineChEBI
SerinChEBI
2-Amino-3-hydroxypropanoateGenerator
2-Amino-3-hydroxypropionateGenerator
Chemical FormulaC3H7NO3
Average Mass105.0926 Da
Monoisotopic Mass105.04259 Da
IUPAC Name2-amino-3-hydroxypropanoic acid
Traditional Nameserin
CAS Registry NumberNot Available
SMILES
NC(CO)C(O)=O
InChI Identifier
InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)
InChI KeyMTCFGRXMJLQNBG-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 22.5 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Abutilon indicumLOTUS Database
Agave americanaLOTUS Database
Allium rotundumLOTUS Database
Antirrhinum majusLOTUS Database
Arabidopsis thalianaLOTUS Database
Bombyx moriLOTUS Database
Castanea sativaLOTUS Database
Chlamydomonas reinhardtiiLOTUS Database
Claviceps purpureaLOTUS Database
Colchicum trigynumLOTUS Database
Glycine maxLOTUS Database
Lates calcariferLOTUS Database
Lemna aequinoctialisLOTUS Database
Litoria verreauxiiLOTUS Database
Lunaria annuaLOTUS Database
Medicago sativaLOTUS Database
Mycoplasma gallisepticumLOTUS Database
Onobrychis kacheticaLOTUS Database
Panax ginsengLOTUS Database
Paris fargesiiLOTUS Database
Populus tremulaLOTUS Database
Puccinia graminisLOTUS Database
Salmonella entericaLOTUS Database
Scolopendra subspinipesLOTUS Database
Solanum lycopersicumLOTUS Database
Stellaria mediaLOTUS Database
Viscum albumLOTUS 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
    • 

  • 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
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
Polarizability9.45 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012739  
KNApSAcK IDC00001393  
Chemspider IDNot Available
KEGG Compound IDC00716  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSerine  
METLIN IDNot Available
PubChem Compound617  
PDB IDNot Available
ChEBI ID17822  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]