Showing NP-Card for L-Serine (NP0001084)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Read more...Show more...Show more...Show more...
Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2022-02-02 01:00:10 UTC
NP-MRD IDNP0001084
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Serine
Description
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0001084 (L-Serine)

     RDKit          2D

 14 13  0  0  0  0  0  0  0  0999 V2000
   -1.0710   -1.4274    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1877   -0.6116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6281    0.6472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4439    1.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4465    0.2043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5525    1.7005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7824   -0.4779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9938   -2.9254    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4801   -0.9131    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0036   -1.8703    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9769   -0.0091    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5218    1.6104    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9419    1.8288    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0411    0.3379    0.0000 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  6
  3 11  1  1
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
Download

3D MOL for NP0001084 (L-Serine)

     RDKit          3D

 14 13  0  0  0  0  0  0  0  0999 V2000
   -1.5921   -0.8790    0.3190 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4304   -0.0408    0.4294 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7965   -0.8544    0.0286 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8882    0.0322    0.1621 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6040    1.1289   -0.4581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6375    1.2678   -1.1514 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4366    2.0729   -0.4892 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4815   -1.7203    0.9142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6331   -1.2004   -0.6900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3460    0.2672    1.4910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6595   -1.1951   -1.0005 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9895   -1.6643    0.7551 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3975    0.1290   -0.6565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5567    2.6562    0.3464 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  5  1  0
  5  6  2  0
  5  2  1  0
  2  1  1  0
  2  3  1  0
  3  4  1  0
  7 14  1  0
  2 10  1  1
  1  8  1  0
  1  9  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
M  END
Download

3D SDF for NP0001084 (L-Serine)

     RDKit          2D

 14 13  0  0  0  0  0  0  0  0999 V2000
   -1.0710   -1.4274    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1877   -0.6116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6281    0.6472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4439    1.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4465    0.2043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5525    1.7005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7824   -0.4779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9938   -2.9254    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4801   -0.9131    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0036   -1.8703    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9769   -0.0091    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5218    1.6104    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9419    1.8288    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0411    0.3379    0.0000 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  6
  3 11  1  1
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
> <DATABASE_ID>
NP0001084

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1

> <INCHI_KEY>
MTCFGRXMJLQNBG-REOHCLBHSA-N

> <FORMULA>
C3H7NO3

> <MOLECULAR_WEIGHT>
105.0926

> <EXACT_MASS>
105.042593095

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
9.386631521233841

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-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>
22.040999999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-serine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001084 (L-Serine)

Download
PDB for NP0001084 (L-Serine)
HEADER    PROTEIN                                 26-OCT-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-OCT-21         0                                  
HETATM    1  H   UNK     0       3.850  -4.001   0.000  0.00  0.00           H+0
HETATM    2  O   UNK     0       4.620  -2.667   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.620  -0.000   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       3.080  -2.667   0.000  0.00  0.00           H+0
HETATM    7  N   UNK     0       1.540  -2.667   0.000  0.00  0.00           N+0
HETATM    8  H   UNK     0       0.003  -2.578   0.000  0.00  0.00           H+0
HETATM    9  H   UNK     0       0.849  -4.044   0.000  0.00  0.00           H+0
HETATM   10  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   11  H   UNK     0       2.827   0.846   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.630   1.537   0.000  0.00  0.00           H+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0      -0.770   1.334   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7   10                                             
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Download
3D PDB for NP0001084 (L-Serine)
Download
SMILES for NP0001084 (L-Serine)
[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])O[H]
Download
INCHI for NP0001084 (L-Serine)
InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1
Download
View in JSmol
Synonyms
Chemical FormulaC3H7NO3
Average Mass105.0926 Da
Monoisotopic Mass105.04259 Da
IUPAC Name(2S)-2-amino-3-hydroxypropanoic acid
Traditional NameL-serine
CAS Registry Number56-45-1
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-/m0/s1
InChI KeyMTCFGRXMJLQNBG-REOHCLBHSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-02-03View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, 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
Escherichia coliKNApSAcK Database
Homo sapiens (Serum)KNApSAcK Database
Homo sapiens (Urine)KNApSAcK 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
    • 

  • L-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 Point228 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility425 mg/mLNot Available
LogP-3.07Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
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 IDHMDB0000187  
DrugBank IDDB00133  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012739  
KNApSAcK IDC00001393  
Chemspider ID5736  
KEGG Compound IDC00065  
BioCyc IDSER  
BiGG ID33717  
Wikipedia LinkL-serine  
METLIN ID5203  
PubChem Compound5951  
PDB IDNot Available
ChEBI ID17115  
Good Scents IDrw1819101  
References
General References