Np mrd loader

Showing NP-Card for iminoribitol (NP0301211)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-09-10 14:01:43 UTC
Updated at2022-09-10 14:01:43 UTC
NP-MRD IDNP0301211
Secondary Accession NumbersNone
Natural Product Identification
Common Nameiminoribitol
Description(2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol belongs to the class of organic compounds known as pyrrolidines. iminoribitol is found in Angylocalyx pynaertii and Morus alba. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms (2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol is a very strong basic compound (based on its pKa).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0301211 (iminoribitol)


  Mrv0541 05041405512D          

 12 12  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6546   -0.3127    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3028    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8474    0.2807    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  6  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  4  8  1  1  0  0  0
  5  9  1  1  0  0  0
  3 10  1  1  0  0  0
  4 11  1  6  0  0  0
  5 12  1  6  0  0  0
M  END
Download

3D MOL for NP0301211 (iminoribitol)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.7051   -0.6902   -0.1009 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0310    0.5310   -0.1141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5845    0.2430   -0.3878 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2339    1.4375   -0.4281 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5949    0.9471   -0.3121 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5335   -0.4362    0.2445 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5916   -1.3427   -0.8297 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0852   -0.5016    0.7483 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3571   -1.7955    0.8805 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1920   -1.3684   -0.5776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1787    1.1079    0.7965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4223    1.0875   -0.9956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4410   -0.2875   -1.3285 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0391    1.9489    0.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0366    0.9643   -1.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1961    1.6040    0.3776 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2545   -0.6588    1.0314 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2129   -1.0448   -1.5329 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0403    0.0923    1.6833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9070   -1.8378    1.7125 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  7  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  1  0
  3  8  1  0
  8  9  1  0
  8  6  1  0
  6 17  1  1
  7 18  1  0
  5 15  1  0
  5 16  1  0
  4 14  1  0
  3 13  1  6
  2 11  1  0
  2 12  1  0
  1 10  1  0
  8 19  1  1
  9 20  1  0
M  END
Download

3D SDF for NP0301211 (iminoribitol)


  Mrv0541 05041405512D          

 12 12  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6546   -0.3127    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3028    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8474    0.2807    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  6  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  4  8  1  1  0  0  0
  5  9  1  1  0  0  0
  3 10  1  1  0  0  0
  4 11  1  6  0  0  0
  5 12  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0301211

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(O)CN[C@]([H])(CO)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/t3-,4+,5-/m1/s1

> <INCHI_KEY>
OQEBIHBLFRADNM-MROZADKFSA-N

> <FORMULA>
C5H11NO3

> <MOLECULAR_WEIGHT>
133.1457

> <EXACT_MASS>
133.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
13.09757469233745

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol

> <ALOGPS_LOGP>
-1.83

> <JCHEM_LOGP>
-2.2554082409999996

> <ALOGPS_LOGS>
0.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.628828479465383

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.318700802503066

> <JCHEM_PKA_STRONGEST_BASIC>
9.360543824381354

> <JCHEM_POLAR_SURFACE_AREA>
72.72

> <JCHEM_REFRACTIVITY>
30.611899999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0301211 (iminoribitol)

Download
PDB for NP0301211 (iminoribitol)
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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   11  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    4    6                                                       
CONECT    2    3    7                                                       
CONECT    3    2    5    6   10                                             
CONECT    4    1    5    8   11                                             
CONECT    5    3    4    9   12                                             
CONECT    6    1    3                                                       
CONECT    7    2                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
CONECT   12    5                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Download
3D PDB for NP0301211 (iminoribitol)
Download
SMILES for NP0301211 (iminoribitol)
[H][C@]1(O)CN[C@]([H])(CO)[C@@]1([H])O
Download
INCHI for NP0301211 (iminoribitol)
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/t3-,4+,5-/m1/s1
Download
View in JSmol
SynonymsNot Available
Chemical FormulaC5H11NO3
Average Mass133.1457 Da
Monoisotopic Mass133.07389 Da
IUPAC Name(2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol
Traditional Name(2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol
CAS Registry NumberNot Available
SMILES
[H][C@]1(O)CN[C@]([H])(CO)[C@@]1([H])O
InChI Identifier
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/t3-,4+,5-/m1/s1
InChI KeyOQEBIHBLFRADNM-MROZADKFSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Angylocalyx pynaertiiLOTUS Database
Morus albaLOTUS Database
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
    • 

  • 1,2-aminoalcohol
    • 

  • Secondary alcohol
    • 

  • Secondary aliphatic amine
    • 

  • Secondary amine
    • 

  • Azacycle
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • 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-1.8ALOGPS
logP-2.3ChemAxon
logS0.69ALOGPS
pKa (Strongest Acidic)13.32ChemAxon
pKa (Strongest Basic)9.36ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area72.72 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.61 m³·mol⁻¹ChemAxon
Polarizability13.1 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 Compound446222  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]