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Showing NP-Card for 2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol (NP0228396)

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Record Information
Version2.0
Created at2022-09-06 08:02:18 UTC
Updated at2022-09-06 08:02:19 UTC
NP-MRD IDNP0228396
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol
Description2,5-Pyrrolidinedimethanol, 3,4-dihydroxy- 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. 2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol is found in Commelina communis, Derris elliptica and Hyacinthoides hispanica. 2,5-Pyrrolidinedimethanol, 3,4-dihydroxy- is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)


  Mrv1533004191518102D          

 11 11  0  0  0  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   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
  1  2  1  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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)

     RDKit          3D

 24 24  0  0  0  0  0  0  0  0999 V2000
   -3.4213   -0.5822    0.3357 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2166   -0.6903    1.0238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1689    0.2335    0.4367 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0884    0.1299    1.1442 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0133   -0.5562    0.3071 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4373   -0.0935    0.4563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9301   -0.2533    1.7455 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5880   -0.2557   -1.1182 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2399    0.8774   -1.6091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9081   -0.0194   -1.0030 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5595   -1.1458   -1.5001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6900    0.3424    0.1849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8868   -1.7449    1.0215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4162   -0.3935    2.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5468    1.2764    0.6108 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4833    1.0821    1.3578 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9158   -1.6458    0.4731 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5296    0.9323    0.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0576   -0.7584   -0.2021 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9324   -0.3381    1.7057 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8289   -1.1284   -1.7448 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8130    1.0709   -2.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1252    0.8823   -1.6201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9180   -1.8808   -1.6722 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
  5  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  3  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  6
  4 16  1  0
  5 17  1  1
  6 18  1  0
  6 19  1  0
  7 20  1  0
  8 21  1  6
  9 22  1  0
 10 23  1  6
 11 24  1  0
M  END
Download

3D SDF for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)


  Mrv1533004191518102D          

 11 11  0  0  0  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   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
  1  2  1  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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0228396

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1NC(CO)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO4/c8-1-3-5(10)6(11)4(2-9)7-3/h3-11H,1-2H2

> <INCHI_KEY>
PFYHYHZGDNWFIF-UHFFFAOYSA-N

> <FORMULA>
C6H13NO4

> <MOLECULAR_WEIGHT>
163.173

> <EXACT_MASS>
163.084457903

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
15.897076144826432

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol

> <ALOGPS_LOGP>
-2.00

> <JCHEM_LOGP>
-2.885743183

> <ALOGPS_LOGS>
0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.394871600783034

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.180374088933199

> <JCHEM_PKA_STRONGEST_BASIC>
8.882975492311811

> <JCHEM_POLAR_SURFACE_AREA>
92.95

> <JCHEM_REFRACTIVITY>
36.5744

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.23e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)

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PDB for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)
HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.267  -1.375   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    3   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)
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SMILES for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)
OCC1NC(CO)C(O)C1O
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INCHI for NP0228396 (2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol)
InChI=1S/C6H13NO4/c8-1-3-5(10)6(11)4(2-9)7-3/h3-11H,1-2H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H13NO4
Average Mass163.1730 Da
Monoisotopic Mass163.08446 Da
IUPAC Name2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol
Traditional Name2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol
CAS Registry NumberNot Available
SMILES
OCC1NC(CO)C(O)C1O
InChI Identifier
InChI=1S/C6H13NO4/c8-1-3-5(10)6(11)4(2-9)7-3/h3-11H,1-2H2
InChI KeyPFYHYHZGDNWFIF-UHFFFAOYSA-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
Commelina communisLOTUS Database
Derris ellipticaLOTUS Database
Scilla campanulataLOTUS 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-2ALOGPS
logP-2.9ChemAxon
logS0.3ALOGPS
pKa (Strongest Acidic)13.18ChemAxon
pKa (Strongest Basic)8.88ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area92.95 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity36.57 m³·mol⁻¹ChemAxon
Polarizability15.9 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 Compound1472  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]