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Showing NP-Card for 4,6-diaminocyclohexane-1,2,3-triol (NP0177786)

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Record Information
Version2.0
Created at2022-09-03 15:40:37 UTC
Updated at2022-09-03 15:40:38 UTC
NP-MRD IDNP0177786
Secondary Accession NumbersNone
Natural Product Identification
Common Name4,6-diaminocyclohexane-1,2,3-triol
Description2-Deoxystreptamine belongs to the class of organic compounds known as aminocyclitols. These are cyclitols with at least one hydroxyl group replace by an amino group. 4,6-diaminocyclohexane-1,2,3-triol is found in Streptomyces lividans. 4,6-diaminocyclohexane-1,2,3-triol was first documented in 2021 (PMID: 34310216). Based on a literature review a small amount of articles have been published on 2-Deoxystreptamine (PMID: 35434630) (PMID: 34967629) (PMID: 33577648) (PMID: 33553900).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0177786 (4,6-diaminocyclohexane-1,2,3-triol)


  Mrv1652309032217402D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 N   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
    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  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 N   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
    0.0000    0.0000    0.0000 C   0  0  0  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
   -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
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for NP0177786 (4,6-diaminocyclohexane-1,2,3-triol)

     RDKit          3D

 25 25  0  0  0  0  0  0  0  0999 V2000
    2.6434    0.7537   -0.3757 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3333    0.3626    0.0281 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2380    1.2424   -0.5655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0372    0.8897    0.1721 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1058    1.7317   -0.3067 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3882   -0.5484   -0.1036 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6292   -0.9003    0.3690 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2758   -1.3977    0.4969 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0068   -1.0019    1.8075 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9809   -1.0605   -0.3148 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9797   -1.9638   -0.0489 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3339    0.8227    0.3982 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9984    0.3100   -1.2366 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2685    0.4707    1.1327 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1118    1.0458   -1.6485 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5169    2.2980   -0.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8609    1.1036    1.2365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8728    2.7145   -0.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9644    1.4658    0.2410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3240   -0.6996   -1.2068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515   -1.5557   -0.2549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5002   -2.4636    0.4957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7928   -0.6879    2.2819 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6920   -1.0740   -1.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6992   -1.8577   -0.7210 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
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  2  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  1
  3 15  1  0
  3 16  1  0
  4 17  1  1
  5 18  1  0
  5 19  1  0
  6 20  1  6
  7 21  1  0
  8 22  1  1
  9 23  1  0
 10 24  1  6
 11 25  1  0
M  END
Download

3D SDF for NP0177786 (4,6-diaminocyclohexane-1,2,3-triol)


  Mrv1652309032217402D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 N   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
    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  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 N   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
    0.0000    0.0000    0.0000 C   0  0  0  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
   -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
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0177786

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H14N2O3/c7-2-1-3(8)5(10)6(11)4(2)9/h2-6,9-11H,1,7-8H2

> <INCHI_KEY>
DTFAJAKTSMLKAT-UHFFFAOYSA-N

> <FORMULA>
C6H14N2O3

> <MOLECULAR_WEIGHT>
162.189

> <EXACT_MASS>
162.100442319

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.246876290645332

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,6-diaminocyclohexane-1,2,3-triol

> <JCHEM_LOGP>
-3.305478564333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
14.004309372165654

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.886817395903687

> <JCHEM_PKA_STRONGEST_BASIC>
9.152200008603737

> <JCHEM_POLAR_SURFACE_AREA>
112.73

> <JCHEM_REFRACTIVITY>
37.9929

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4,6-diaminocyclohexane-1,2,3-triol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0177786 (4,6-diaminocyclohexane-1,2,3-triol)

Download
PDB for NP0177786 (4,6-diaminocyclohexane-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  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    2   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 NP0177786 (4,6-diaminocyclohexane-1,2,3-triol)
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SMILES for NP0177786 (4,6-diaminocyclohexane-1,2,3-triol)
NC1CC(N)C(O)C(O)C1O
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INCHI for NP0177786 (4,6-diaminocyclohexane-1,2,3-triol)
InChI=1S/C6H14N2O3/c7-2-1-3(8)5(10)6(11)4(2)9/h2-6,9-11H,1,7-8H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H14N2O3
Average Mass162.1890 Da
Monoisotopic Mass162.10044 Da
IUPAC Name4,6-diaminocyclohexane-1,2,3-triol
Traditional Name4,6-diaminocyclohexane-1,2,3-triol
CAS Registry NumberNot Available
SMILES
NC1CC(N)C(O)C(O)C1O
InChI Identifier
InChI=1S/C6H14N2O3/c7-2-1-3(8)5(10)6(11)4(2)9/h2-6,9-11H,1,7-8H2
InChI KeyDTFAJAKTSMLKAT-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 lividansLOTUS 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
    • 

  • Cyclohexylamine
    • 

  • Cyclohexanol
    • 

  • Secondary alcohol
    • 

  • 1,2-aminoalcohol
    • 

  • Polyol
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Amine
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
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-3.3ChemAxon
pKa (Strongest Acidic)12.89ChemAxon
pKa (Strongest Basic)9.15ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area112.73 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.99 m³·mol⁻¹ChemAxon
Polarizability16.25 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0245101  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID89384  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound98959  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Tran TPA, Poulet S, Pernak M, Rayar A, Azoulay S, Di Giorgio A, Duca M: Development of 2-deoxystreptamine-nucleobase conjugates for the inhibition of oncogenic miRNA production. RSC Med Chem. 2021 Dec 16;13(3):311-319. doi: 10.1039/d1md00345c. eCollection 2022 Mar 23. [PubMed:35434630  ] 
  2. Guo J, Liu S, Pang Q, Zhang H, Gao L, Chen L, Song Z: Synthesis of Silacyclohexanones from Divinylsilanes and Allylamines by a Rh-Catalyzed Cyclization. Org Lett. 2022 Jan 21;24(2):726-730. doi: 10.1021/acs.orglett.1c04183. Epub 2021  Dec 30. [PubMed:34967629  ] 
  3. Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y: Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother. 2021 Sep 17;65(10):e0100921. doi: 10.1128/AAC.01009-21. Epub 2021 Jul 26. [PubMed:34310216  ] 
  4. Kudo F, Mori A, Koide M, Yajima R, Takeishi R, Miyanaga A, Eguchi T: One-pot enzymatic synthesis of 2-deoxy-scyllo-inosose from d-glucose and polyphosphate. Biosci Biotechnol Biochem. 2021 Jan 7;85(1):108-114. doi: 10.1093/bbb/zbaa025. [PubMed:33577648  ] 
  5. Alkhzem AH, Woodman TJ, Blagbrough IS: Multinuclear Nuclear Magnetic Resonance Spectroscopy Is Used to Determine Rapidly and Accurately the Individual pK a Values of 2-Deoxystreptamine, Neamine, Neomycin, Paromomycin, and Streptomycin. ACS Omega. 2021 Jan 20;6(4):2824-2835. doi: 10.1021/acsomega.0c05138. eCollection 2021 Feb 2. [PubMed:33553900  ] 
  6. LOTUS database [Link]