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Showing NP-Card for 2-Amino-1,3-propanediol (NP0084508)

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Record Information
Version2.0
Created at2022-04-29 05:13:51 UTC
Updated at2022-04-29 05:13:51 UTC
NP-MRD IDNP0084508
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Amino-1,3-propanediol
Description2-Amino-1,3-propanediol, also known as serinol or 2-aminopropane-1,3-diol, belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom. 2-Amino-1,3-propanediol is found in Saccharum officinarum . 2-Amino-1,3-propanediol is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0084508 (2-Amino-1,3-propanediol)


  Mrv0541 05041411042D          

  6  5  0  0  0  0            999 V2000
    2.0625   -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
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    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
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
M  END
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3D MOL for NP0084508 (2-Amino-1,3-propanediol)

     RDKit          3D

 15 14  0  0  0  0  0  0  0  0999 V2000
    0.2126   -1.3444   -0.0865 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0743    0.0594    0.1657 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2329    0.7824   -0.4560 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3880    0.2513    0.1665 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2642    0.5782   -0.2737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2355   -0.1291    0.4542 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6939   -1.4913   -1.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6858   -1.8673   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1415    0.2555    1.2742 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3349    0.5985   -1.5406 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2513    1.8697   -0.1971 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2116   -0.7350    0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4277    0.4644   -1.3620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3773    1.6399   -0.0319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5503   -0.9320   -0.0139 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  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
M  END
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3D SDF for NP0084508 (2-Amino-1,3-propanediol)


  Mrv0541 05041411042D          

  6  5  0  0  0  0            999 V2000
    2.0625   -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
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    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
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084508

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CO)CO

> <INCHI_IDENTIFIER>
InChI=1S/C3H9NO2/c4-3(1-5)2-6/h3,5-6H,1-2,4H2

> <INCHI_KEY>
KJJPLEZQSCZCKE-UHFFFAOYSA-N

> <FORMULA>
C3H9NO2

> <MOLECULAR_WEIGHT>
91.1091

> <EXACT_MASS>
91.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
9.38345914394807

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-aminopropane-1,3-diol

> <ALOGPS_LOGP>
-1.79

> <JCHEM_LOGP>
-1.9458958193333333

> <ALOGPS_LOGS>
1.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.454272624159358

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.752636093996717

> <JCHEM_PKA_STRONGEST_BASIC>
9.22907809135089

> <JCHEM_POLAR_SURFACE_AREA>
66.48

> <JCHEM_REFRACTIVITY>
22.173599999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.04e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-aminopropane-1,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0084508 (2-Amino-1,3-propanediol)

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PDB for NP0084508 (2-Amino-1,3-propanediol)
HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         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
CONECT    1    3    5                                                       
CONECT    2    3    6                                                       
CONECT    3    1    2    4                                                  
CONECT    4    3                                                            
CONECT    5    1                                                            
CONECT    6    2                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END

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3D PDB for NP0084508 (2-Amino-1,3-propanediol)
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SMILES for NP0084508 (2-Amino-1,3-propanediol)
NC(CO)CO
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INCHI for NP0084508 (2-Amino-1,3-propanediol)
InChI=1S/C3H9NO2/c4-3(1-5)2-6/h3,5-6H,1-2,4H2
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Synonyms
ValueSource
Serinol, (+-)-isomerMeSH
SerinolMeSH
2-Aminopropane-1,3-diolMeSH
Chemical FormulaC3H9NO2
Average Mass91.1091 Da
Monoisotopic Mass91.06333 Da
IUPAC Name2-aminopropane-1,3-diol
Traditional Name2-aminopropane-1,3-diol
CAS Registry NumberNot Available
SMILES
NC(CO)CO
InChI Identifier
InChI=1S/C3H9NO2/c4-3(1-5)2-6/h3,5-6H,1-2,4H2
InChI KeyKJJPLEZQSCZCKE-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Saccharum officinarumPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom.
KingdomOrganic compounds  
Super ClassOrganic nitrogen compounds  
ClassOrganonitrogen compounds  
Sub ClassAmines  
Direct Parent1,2-aminoalcohols  
Alternative Parents
Substituents
  • 1,2-aminoalcohol
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Primary aliphatic amine
    • 

  • Alcohol
    • 

  • 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-1.8ALOGPS
logP-1.9ChemAxon
logS1.06ALOGPS
pKa (Strongest Acidic)14.75ChemAxon
pKa (Strongest Basic)9.23ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area66.48 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.17 m³·mol⁻¹ChemAxon
Polarizability9.38 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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound68294  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available