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Showing NP-Card for 5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol (NP0330958)

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Record Information
Version2.0
Created at2022-09-12 16:48:55 UTC
Updated at2022-09-12 16:48:55 UTC
NP-MRD IDNP0330958
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
Description5-Amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol belongs to the class of organic compounds known as aminocyclitols. These are cyclitols with at least one hydroxyl group replace by an amino group. 5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol is found in Streptomyces hygroscopicus. 5-Amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)


  Mrv1533004231522462D          

 13 13  0  0  0  0            999 V2000
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9626    2.6447    0.0000 O   0  0  0  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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  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  0  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
  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  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
Download

3D MOL for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)

     RDKit          3D

 28 28  0  0  0  0  0  0  0  0999 V2000
   -1.9189   -1.7600   -0.5639 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8504   -1.0849    0.1590 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2997   -0.9167   -0.7608 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2302    0.1947   -0.4335 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0777    0.3726   -1.5460 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1613   -0.1911    0.7194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8479   -1.3547    0.4283 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5875    1.4896   -0.0963 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1247    2.0407    1.0860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8934    1.4258    0.0744 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5881    1.5808   -1.1413 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3848    0.1785    0.7436 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7924    0.2002    0.6473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6305   -2.0414   -1.5258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3692   -2.5019   -0.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5448   -1.7478    1.0073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0902   -0.7475   -1.7911 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8942   -1.8712   -0.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4556   -0.5369   -1.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6080   -0.2060    1.6589 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9259    0.6388    0.7553 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4846   -2.1240    0.9225 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7864    2.2734   -0.8851 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4319    2.3648    1.6937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2012    2.2858    0.7218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4808    1.9328   -0.9228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1835    0.2462    1.8484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9875   -0.1405   -0.2827 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  6
  4  6  1  0
  6  7  1  0
  4  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  2  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  1
  3 17  1  0
  3 18  1  0
  5 19  1  0
  6 20  1  0
  6 21  1  0
  7 22  1  0
  8 23  1  6
  9 24  1  0
 10 25  1  1
 11 26  1  0
 12 27  1  1
 13 28  1  0
M  END
Download

3D SDF for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)


  Mrv1533004231522462D          

 13 13  0  0  0  0            999 V2000
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9626    2.6447    0.0000 O   0  0  0  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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  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  0  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
  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  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0330958

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1CC(O)(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H15NO5/c8-3-1-7(13,2-9)6(12)5(11)4(3)10/h3-6,9-13H,1-2,8H2

> <INCHI_KEY>
VDLOJRUTNRJDJO-UHFFFAOYSA-N

> <FORMULA>
C7H15NO5

> <MOLECULAR_WEIGHT>
193.199

> <EXACT_MASS>
193.095022587

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
18.46010220759988

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol

> <ALOGPS_LOGP>
-2.46

> <JCHEM_LOGP>
-3.964930066

> <ALOGPS_LOGS>
0.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.279976971457813

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.459021436657949

> <JCHEM_PKA_STRONGEST_BASIC>
8.509558905930348

> <JCHEM_POLAR_SURFACE_AREA>
127.17000000000002

> <JCHEM_REFRACTIVITY>
42.51729999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.30e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)

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PDB for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)
HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+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   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.344   3.490   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.797   4.937   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6    8                                             
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6                                                            
CONECT    8    4    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    2   13                                                  
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

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3D PDB for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)
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SMILES for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)
NC1CC(O)(CO)C(O)C(O)C1O
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INCHI for NP0330958 (5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol)
InChI=1S/C7H15NO5/c8-3-1-7(13,2-9)6(12)5(11)4(3)10/h3-6,9-13H,1-2,8H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H15NO5
Average Mass193.1990 Da
Monoisotopic Mass193.09502 Da
IUPAC Name5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
Traditional Name5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
CAS Registry NumberNot Available
SMILES
NC1CC(O)(CO)C(O)C(O)C1O
InChI Identifier
InChI=1S/C7H15NO5/c8-3-1-7(13,2-9)6(12)5(11)4(3)10/h3-6,9-13H,1-2,8H2
InChI KeyVDLOJRUTNRJDJO-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
Streptomyces hygroscopicusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aminocyclitols. These are cyclitols with at least one hydroxyl group replace by an amino group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct ParentAminocyclitols  
Alternative Parents
Substituents
  • Aminocyclitol
    • 

  • Cyclohexanol
    • 

  • Cyclohexylamine
    • 

  • Tertiary alcohol
    • 

  • 1,2-aminoalcohol
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Organic nitrogen compound
    • 

  • Primary alcohol
    • 

  • Primary amine
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Amine
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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-2.5ALOGPS
logP-4ChemAxon
logS0.63ALOGPS
pKa (Strongest Acidic)12.46ChemAxon
pKa (Strongest Basic)8.51ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area127.17 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity42.52 m³·mol⁻¹ChemAxon
Polarizability18.46 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
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 Compound13137289  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]