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Showing NP-Card for (+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine (NP0074950)

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Record Information
Version1.0
Created at2022-04-28 20:14:42 UTC
Updated at2022-04-28 20:14:42 UTC
NP-MRD IDNP0074950
Secondary Accession NumbersNone
Natural Product Identification
Common Name(+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine
Description2-Pyrrolidinemethanol, 3-hydroxy-, (2R,3S)- belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. (+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine is found in Castanospermum australe . 2-Pyrrolidinemethanol, 3-hydroxy-, (2R,3S)- is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)


  Mrv1652310111718122D          

  8  8  0  0  0  0            999 V2000
   -2.4330    1.4160    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1004    0.9310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8455    0.1464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0205    0.1464    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7656    0.9310    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9810    1.1859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3679    0.6339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5356   -0.5209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  4  8  1  1  0  0  0
M  END
Download

3D MOL for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)

     RDKit          3D

 19 19  0  0  0  0  0  0  0  0999 V2000
    2.2074    1.1872    0.1905 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9055    0.0589   -0.5425 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5049   -0.4299   -0.3134 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2531   -0.7746    1.0653 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1351   -0.5140    1.3336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7527   -0.1396   -0.0134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5412    0.6071   -0.5892 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6939    0.9040   -1.9171 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8467    1.0240    0.9229 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5907   -0.7525   -0.1782 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0865    0.1880   -1.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3117   -1.2907   -0.9695 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5485   -1.7366    1.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6658   -1.3397    1.8223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2112    0.4259    1.9530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6270    0.4897    0.0792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8539   -1.0509   -0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4208    1.5053    0.0534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3535    1.6384   -1.9908 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  1  0
  6  7  1  0
  7  8  1  0
  7  3  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  6
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  1
  8 19  1  0
M  END
Download

3D SDF for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)


  Mrv1652310111718122D          

  8  8  0  0  0  0            999 V2000
   -2.4330    1.4160    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1004    0.9310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8455    0.1464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0205    0.1464    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7656    0.9310    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9810    1.1859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3679    0.6339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5356   -0.5209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  4  8  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0074950

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1NCC[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO2/c7-3-4-5(8)1-2-6-4/h4-8H,1-3H2/t4-,5+/m1/s1

> <INCHI_KEY>
TYLFLHPQWQQWRD-UHNVWZDZSA-N

> <FORMULA>
C5H11NO2

> <MOLECULAR_WEIGHT>
117.148

> <EXACT_MASS>
117.078978598

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.295333857732496

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-2-(hydroxymethyl)pyrrolidin-3-ol

> <ALOGPS_LOGP>
-1.33

> <JCHEM_LOGP>
-1.56511356

> <ALOGPS_LOGS>
0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.24753709743226

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.379323518188635

> <JCHEM_PKA_STRONGEST_BASIC>
10.064742118692168

> <JCHEM_POLAR_SURFACE_AREA>
52.489999999999995

> <JCHEM_REFRACTIVITY>
29.514799999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.77e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-2-(hydroxymethyl)pyrrolidin-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)

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PDB for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)
HEADER    PROTEIN                                 11-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-OCT-17         0                                  
HETATM    1  N   UNK     0      -4.542   2.643   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -5.787   1.738   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.312   0.273   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.772   0.273   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.296   1.738   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.831   2.214   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.687   1.183   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.866  -0.972   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    3    1                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    4                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)
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SMILES for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)
OC[C@H]1NCC[C@@H]1O
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INCHI for NP0074950 ((+)-2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidine)
InChI=1S/C5H11NO2/c7-3-4-5(8)1-2-6-4/h4-8H,1-3H2/t4-,5+/m1/s1
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Synonyms
ValueSource
(2R,3S)-3-Hydroxy-2-pyrrolidinemethanolPhytoBank
(2R,3S)-2-(Hydroxymethyl)-3-hydroxypyrrolidinePhytoBank
(2R,3S)-2-(Hydroxymethyl)pyrrolidin-3-olPhytoBank
(2R,3S)-3-Hydroxy-2-hydroxymethylpyrrolidinePhytoBank
2R-Hydroxymethyl-3S-hydroxypyrolidinePhytoBank
CYB 3PhytoBank
CYB-3PhytoBank
Chemical FormulaC5H11NO2
Average Mass117.1480 Da
Monoisotopic Mass117.07898 Da
IUPAC Name(2R,3S)-2-(hydroxymethyl)pyrrolidin-3-ol
Traditional Name(2R,3S)-2-(hydroxymethyl)pyrrolidin-3-ol
CAS Registry NumberNot Available
SMILES
OC[C@H]1NCC[C@@H]1O
InChI Identifier
InChI=1S/C5H11NO2/c7-3-4-5(8)1-2-6-4/h4-8H,1-3H2/t4-,5+/m1/s1
InChI KeyTYLFLHPQWQQWRD-UHNVWZDZSA-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
Castanospermum australePlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrrolidines  
Sub ClassNot Available
Direct ParentPyrrolidines  
Alternative Parents
Substituents
  • Pyrrolidine
    • 

  • Secondary alcohol
    • 

  • 1,2-aminoalcohol
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Secondary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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-1.3ALOGPS
logP-1.6ChemAxon
logS0.82ALOGPS
pKa (Strongest Acidic)14.38ChemAxon
pKa (Strongest Basic)10.06ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area52.49 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.51 m³·mol⁻¹ChemAxon
Polarizability12.3 ųChemAxon
Number of Rings1ChemAxon
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 Compound11073391  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available