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Showing NP-Card for 1-Deoxythreitol (NP0074898)

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Record Information
Version2.0
Created at2022-04-28 20:12:38 UTC
Updated at2022-04-28 20:12:38 UTC
NP-MRD IDNP0074898
Secondary Accession NumbersNone
Natural Product Identification
Common Name1-Deoxythreitol
Description1-Deoxy-D-threitol belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl). 1-Deoxythreitol is found in Foeniculum vulgare and Pimpinella anisum L. . Based on a literature review very few articles have been published on 1-Deoxy-D-threitol.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0074898 (1-Deoxythreitol)


  Mrv1652304282222122D          

  7  6  0  0  1  0            999 V2000
    0.8250   -1.4289    0.0000 O   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    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    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
  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
  4  6  1  1  0  0  0
  3  7  1  1  0  0  0
M  END
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3D MOL for NP0074898 (1-Deoxythreitol)

     RDKit          3D

 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.2092   -1.2083    0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9400    0.2575   -0.0504 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7716    0.9218    0.8518 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4612    0.6691    0.2273 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5501    2.0505    0.0585 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4886    0.0114   -0.6533 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4395   -1.3810   -0.5199 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7842   -1.6339    1.0102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8705   -1.8130   -0.7632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3218   -1.3348    0.1622 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2053    0.5861   -1.0802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3244    1.1110    1.7118 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7131    0.4529    1.2843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1681    2.4137   -0.5132 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4061    0.2829   -1.7072 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5005    0.3134   -0.3098 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0360   -1.6993    0.2135 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  4 13  1  1
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
M  END
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3D SDF for NP0074898 (1-Deoxythreitol)


  Mrv1652304282222122D          

  7  6  0  0  1  0            999 V2000
    0.8250   -1.4289    0.0000 O   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    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    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
  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
  4  6  1  1  0  0  0
  3  7  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0074898

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H10O3/c1-3(6)4(7)2-5/h3-7H,2H2,1H3/t3-,4-/m1/s1

> <INCHI_KEY>
YAXKTBLXMTYWDQ-QWWZWVQMSA-N

> <FORMULA>
C4H10O3

> <MOLECULAR_WEIGHT>
106.121

> <EXACT_MASS>
106.062994182

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
10.760812105377513

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-butane-1,2,3-triol

> <ALOGPS_LOGP>
-1.75

> <JCHEM_LOGP>
-1.4224389979999998

> <ALOGPS_LOGS>
0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.060910413712342

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.38427309510853

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9717943057235576

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
24.9349

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.96e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-butane-1,2,3-triol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0074898 (1-Deoxythreitol)

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PDB for NP0074898 (1-Deoxythreitol)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END

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3D PDB for NP0074898 (1-Deoxythreitol)
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SMILES for NP0074898 (1-Deoxythreitol)
C[C@@H](O)[C@H](O)CO
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INCHI for NP0074898 (1-Deoxythreitol)
InChI=1S/C4H10O3/c1-3(6)4(7)2-5/h3-7H,2H2,1H3/t3-,4-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC4H10O3
Average Mass106.1210 Da
Monoisotopic Mass106.06299 Da
IUPAC Name(2R,3R)-butane-1,2,3-triol
Traditional Name(2R,3R)-butane-1,2,3-triol
CAS Registry NumberNot Available
SMILES
C[C@@H](O)[C@H](O)CO
InChI Identifier
InChI=1S/C4H10O3/c1-3(6)4(7)2-5/h3-7H,2H2,1H3/t3-,4-/m1/s1
InChI KeyYAXKTBLXMTYWDQ-QWWZWVQMSA-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
Foeniculum vulgareLOTUS Database
Pimpinella anisumPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct ParentSecondary alcohols  
Alternative Parents
Substituents
  • Secondary alcohol
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-1.4ChemAxon
logS0.97ALOGPS
pKa (Strongest Acidic)13.38ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity24.93 m³·mol⁻¹ChemAxon
Polarizability10.76 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 ID4911109  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6398419  
PDB IDNot Available
ChEBI ID179049  
Good Scents IDNot Available
References
General ReferencesNot Available