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Showing NP-Card for (2r,3r,4r)-pentane-1,2,3,4-tetrol (NP0266338)

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Record Information
Version1.0
Created at2022-09-08 10:39:16 UTC
Updated at2022-09-08 10:39:16 UTC
NP-MRD IDNP0266338
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3r,4r)-pentane-1,2,3,4-tetrol
Description(2R,3R,4R)-pentane-1,2,3,4-tetrol belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions. (2r,3r,4r)-pentane-1,2,3,4-tetrol is found in Glehnia littoralis. Based on a literature review very few articles have been published on (2R,3R,4R)-pentane-1,2,3,4-tetrol.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)


  Mrv1652309082212392D          

  9  8  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  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
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    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  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
Download

3D MOL for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
    2.1886    0.4063    0.5677 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5285   -0.2195   -0.6243 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2285   -1.3983   -0.9120 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0971   -0.5977   -0.3980 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0538   -1.4853    0.6544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8220    0.5650   -0.2102 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5926    1.2681    0.9550 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2428    0.0060   -0.1211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1652    1.0448    0.0075 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2698   -0.3262    1.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2403    0.6236    0.2853 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7423    1.3528    0.8872 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6104    0.4699   -1.4672 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6380   -2.1821   -0.9716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2415   -1.1407   -1.3172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1551   -0.9999    1.4963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7784    1.2216   -1.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9850    0.8685    1.7514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3479   -0.6762    0.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4876   -0.5855   -1.0447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9817    1.7847   -0.6040 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
  6  8  1  0
  8  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  4 15  1  6
  5 16  1  0
  6 17  1  6
  7 18  1  0
  8 19  1  0
  8 20  1  0
  9 21  1  0
M  END
Download

3D SDF for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)


  Mrv1652309082212392D          

  9  8  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  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
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    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  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0266338

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O4/c1-3(7)5(9)4(8)2-6/h3-9H,2H2,1H3/t3-,4-,5-/m1/s1

> <INCHI_KEY>
FJGNTEKSQVNVTJ-UOWFLXDJSA-N

> <FORMULA>
C5H12O4

> <MOLECULAR_WEIGHT>
136.147

> <EXACT_MASS>
136.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.453429981111968

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-pentane-1,2,3,4-tetrol

> <JCHEM_LOGP>
-2.05277394

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.194937901081996

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.933563962264053

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9741397070086384

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
30.897399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R)-pentane-1,2,3,4-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)

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PDB for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)
HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)
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SMILES for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)
C[C@@H](O)[C@@H](O)[C@H](O)CO
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INCHI for NP0266338 ((2r,3r,4r)-pentane-1,2,3,4-tetrol)
InChI=1S/C5H12O4/c1-3(7)5(9)4(8)2-6/h3-9H,2H2,1H3/t3-,4-,5-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H12O4
Average Mass136.1470 Da
Monoisotopic Mass136.07356 Da
IUPAC Name(2R,3R,4R)-pentane-1,2,3,4-tetrol
Traditional Name(2R,3R,4R)-pentane-1,2,3,4-tetrol
CAS Registry NumberNot Available
SMILES
C[C@@H](O)[C@@H](O)[C@H](O)CO
InChI Identifier
InChI=1S/C5H12O4/c1-3(7)5(9)4(8)2-6/h3-9H,2H2,1H3/t3-,4-,5-/m1/s1
InChI KeyFJGNTEKSQVNVTJ-UOWFLXDJSA-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
Glehnia littoralisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct Parent1,2-diols  
Alternative Parents
Substituents
  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • 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-2.1ChemAxon
pKa (Strongest Acidic)12.93ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area80.92 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity30.9 m³·mol⁻¹ChemAxon
Polarizability13.45 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 ID73987229  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53802272  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]