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Showing NP-Card for (1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol (NP0164387)

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Record Information
Version2.0
Created at2022-09-02 23:15:17 UTC
Updated at2022-09-02 23:15:17 UTC
NP-MRD IDNP0164387
Secondary Accession NumbersNone
Natural Product Identification
Common Name(1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol
Description (1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol is found in Streptomyces lincolnensis.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)


  Mrv1652309032201152D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
  3 11  1  0  0  0  0
M  END
Download

3D MOL for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)

     RDKit          3D

 25 25  0  0  0  0  0  0  0  0999 V2000
    3.2035    0.1064   -0.9535 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2020    0.9586   -0.5375 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1062    0.2010    0.2252 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0796    1.1681    0.6346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3079    0.6719    0.7707 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1798    1.7710    0.5820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7196   -0.3784   -0.1944 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8845   -0.9936    0.3159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6945   -1.4536   -0.3539 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7038   -2.3404    0.7186 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6762   -0.9345   -0.6156 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1587   -0.7755   -0.5151 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6184    1.7816    0.1032 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7168    1.4413   -1.3936 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6236   -0.2022    1.1409 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3811    1.6154    1.6243 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0907    2.0501   -0.0685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4929    0.3199    1.8043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7236    2.4607    0.0533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9640    0.0779   -1.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5952   -0.3272    0.3951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959   -2.0613   -1.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171   -2.6665    0.8565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7968   -0.6994   -1.7045 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3910   -1.7911   -0.4417 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
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11  3  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  1
  4 16  1  0
  4 17  1  0
  5 18  1  1
  6 19  1  0
  7 20  1  6
  8 21  1  0
  9 22  1  6
 10 23  1  0
 11 24  1  0
 11 25  1  0
M  END
Download

3D SDF for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)


  Mrv1652309032201152D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
  3 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0164387

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1C[C@@H](O)[C@H](O)[C@H](O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H14O4/c8-3-4-1-5(9)7(11)6(10)2-4/h4-11H,1-3H2/t4-,5-,6-,7-/m1/s1

> <INCHI_KEY>
AMQCFCSHASFWRD-DBRKOABJSA-N

> <FORMULA>
C7H14O4

> <MOLECULAR_WEIGHT>
162.185

> <EXACT_MASS>
162.089208931

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.516104585224728

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3R)-5-(hydroxymethyl)cyclohexane-1,2,3-triol

> <ALOGPS_LOGP>
-1.68

> <JCHEM_LOGP>
-1.9408195413333333

> <ALOGPS_LOGS>
0.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.562462584459968

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.133916705327419

> <JCHEM_PKA_STRONGEST_BASIC>
-2.5965716136422783

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
38.398799999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.56e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R)-5-(hydroxymethyl)cyclohexane-1,2,3-triol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)

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PDB for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)
HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    3                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)
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SMILES for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)
OC[C@H]1C[C@@H](O)[C@H](O)[C@H](O)C1
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INCHI for NP0164387 ((1r,2r,3r,5r)-5-(hydroxymethyl)cyclohexane-1,2,3-triol)
InChI=1S/C7H14O4/c8-3-4-1-5(9)7(11)6(10)2-4/h4-11H,1-3H2/t4-,5-,6-,7-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H14O4
Average Mass162.1850 Da
Monoisotopic Mass162.08921 Da
IUPAC Name(1R,3R)-5-(hydroxymethyl)cyclohexane-1,2,3-triol
Traditional Name(1R,3R)-5-(hydroxymethyl)cyclohexane-1,2,3-triol
CAS Registry NumberNot Available
SMILES
OC[C@H]1C[C@@H](O)[C@H](O)[C@H](O)C1
InChI Identifier
InChI=1S/C7H14O4/c8-3-4-1-5(9)7(11)6(10)2-4/h4-11H,1-3H2/t4-,5-,6-,7-/m1/s1
InChI KeyAMQCFCSHASFWRD-DBRKOABJSA-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
Streptomyces lincolnensisLOTUS Database
Chemical Taxonomy
ClassificationNot classified
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-1.7ALOGPS
logP-1.9ChemAxon
logS0.61ALOGPS
pKa (Strongest Acidic)13.13ChemAxon
pKa (Strongest Basic)-2.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area80.92 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity38.4 m³·mol⁻¹ChemAxon
Polarizability16.52 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
External LinksNot Available
References
General References
  1. LOTUS database [Link]