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Showing NP-Card for daunosamine (NP0290252)

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Record Information
Version2.0
Created at2022-09-09 20:51:00 UTC
Updated at2022-09-09 20:51:00 UTC
NP-MRD IDNP0290252
Secondary Accession NumbersNone
Natural Product Identification
Common Namedaunosamine
DescriptionDaunosamine belongs to the class of organic compounds known as 1,3-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C3 atom. daunosamine is found in Streptomyces peucetius. daunosamine was first documented in 2020 (PMID: 33399122). Based on a literature review a small amount of articles have been published on daunosamine (PMID: 34751552) (PMID: 34744202) (PMID: 33021304) (PMID: 32992248).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0290252 (daunosamine)


  Mrv1652309092222512D          

 10  9  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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  1  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
  9 10  2  0  0  0  0
M  END
Download

3D MOL for NP0290252 (daunosamine)

     RDKit          3D

 23 22  0  0  0  0  0  0  0  0999 V2000
   -2.6336    0.5369    0.0772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3029   -0.0564   -0.3179 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4994   -1.3441   -0.7329 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2620    0.1017    0.7457 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6835   -0.6632    1.8605 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0922   -0.3549    0.3855 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1250   -1.7806    0.0324 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7994    0.3994   -0.6710 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0218    1.8206   -0.3756 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6844    2.4030    0.6337 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4931   -0.0172   -0.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7501    1.5934   -0.2716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8256    0.4924    1.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9471    0.5384   -1.2070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7800   -1.3272   -1.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2168    1.1409    1.1146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0015   -1.5688    1.5515 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7248   -0.2914    1.3185 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2496   -2.3705    0.8970 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9845   -1.9450   -0.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3513    0.3268   -1.6781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8236   -0.0691   -0.7779 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5390    2.4351   -1.1207 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
  9 10  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  3 15  1  0
  4 16  1  1
  5 17  1  0
  6 18  1  1
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
M  END
Download

3D SDF for NP0290252 (daunosamine)


  Mrv1652309092222512D          

 10  9  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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  1  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
  9 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0290252

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](O)[C@@H](O)[C@@H](N)CC=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO3/c1-4(9)6(10)5(7)2-3-8/h3-6,9-10H,2,7H2,1H3/t4-,5-,6+/m0/s1

> <INCHI_KEY>
WPJRFCZKZXBUNI-HCWXCVPCSA-N

> <FORMULA>
C6H13NO3

> <MOLECULAR_WEIGHT>
147.174

> <EXACT_MASS>
147.089543283

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
14.840274373831406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,5S)-3-amino-4,5-dihydroxyhexanal

> <JCHEM_LOGP>
-1.9131739323333337

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.072456133287726

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.532724028070355

> <JCHEM_PKA_STRONGEST_BASIC>
8.961072632929515

> <JCHEM_POLAR_SURFACE_AREA>
83.55000000000001

> <JCHEM_REFRACTIVITY>
36.1212

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
daunosamine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0290252 (daunosamine)

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PDB for NP0290252 (daunosamine)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       7.287   1.127   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.288   3.437   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   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0290252 (daunosamine)
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SMILES for NP0290252 (daunosamine)
C[C@H](O)[C@@H](O)[C@@H](N)CC=O
Download
INCHI for NP0290252 (daunosamine)
InChI=1S/C6H13NO3/c1-4(9)6(10)5(7)2-3-8/h3-6,9-10H,2,7H2,1H3/t4-,5-,6+/m0/s1
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View in JSmol
Synonyms
ValueSource
3-Amino-2,3,6-trideoxy-L-lyxo-hexoseChEBI
6,6,6-Trifluoro-L-daunosamineMeSH
Daunosamine hydrochlorideMeSH
Chemical FormulaC6H13NO3
Average Mass147.1740 Da
Monoisotopic Mass147.08954 Da
IUPAC Name(3S,4S,5S)-3-amino-4,5-dihydroxyhexanal
Traditional Namedaunosamine
CAS Registry NumberNot Available
SMILES
C[C@H](O)[C@@H](O)[C@@H](N)CC=O
InChI Identifier
InChI=1S/C6H13NO3/c1-4(9)6(10)5(7)2-3-8/h3-6,9-10H,2,7H2,1H3/t4-,5-,6+/m0/s1
InChI KeyWPJRFCZKZXBUNI-HCWXCVPCSA-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 peucetiusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C3 atom.
KingdomOrganic compounds  
Super ClassOrganic nitrogen compounds  
ClassOrganonitrogen compounds  
Sub ClassAmines  
Direct Parent1,3-aminoalcohols  
Alternative Parents
Substituents
  • 1,3-aminoalcohol
    • 

  • Alpha-hydrogen aldehyde
    • 

  • 1,2-aminoalcohol
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Organic oxygen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Aldehyde
    • 

  • Alcohol
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-1.9ChemAxon
pKa (Strongest Acidic)13.53ChemAxon
pKa (Strongest Basic)8.96ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity36.12 m³·mol⁻¹ChemAxon
Polarizability14.84 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 ID140755  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDaunosamine  
METLIN IDNot Available
PubChem Compound160128  
PDB IDNot Available
ChEBI ID32539  
Good Scents IDNot Available
References
General References
  1. Mohideen FI, Nguyen LH, Richard JD, Ouadhi S, Kwan DH: In Vitro Reconstitution of the dTDP-l-Daunosamine Biosynthetic Pathway Provides Insights into Anthracycline Glycosylation. ACS Chem Biol. 2021 Nov 9. doi: 10.1021/acschembio.1c00646. [PubMed:34751552  ] 
  2. Li M, Zhang Z: The snogI Gene is Necessary for the Proper Functioning of the Nogalamycin Biosynthesis Pathway. Indian J Microbiol. 2021 Dec;61(4):467-474. doi: 10.1007/s12088-021-00941-7. Epub 2021 May 7. [PubMed:34744202  ] 
  3. Khan A, Kumar Sahu N: Folate encapsulation in PEG-diamine grafted mesoporous Fe3O4 nanoparticles for hyperthermia and in vitro assessment. IET Nanobiotechnol. 2020 Dec;14(9):881-888. doi: 10.1049/iet-nbt.2020.0101. [PubMed:33399122  ] 
  4. Sinha R, Purkayastha P: Daunomycin delivery by ultrasmall graphene quantum dots to DNA duplexes: understanding the dynamics by resonance energy transfer. J Mater Chem B. 2020 Nov 14;8(42):9756-9763. doi: 10.1039/d0tb01831g. Epub 2020 Oct 6. [PubMed:33021304  ] 
  5. Barthwal R, Raje S, Pandav K: Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4 by anticancer drug epirubicin. Bioorg Med Chem. 2020 Dec 1;28(23):115761. doi: 10.1016/j.bmc.2020.115761. Epub 2020 Sep 10. [PubMed:32992248  ] 
  6. LOTUS database [Link]