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Showing NP-Card for 2,4,5-trihydroxy-3-methoxypentanal (NP0246452)

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Record Information
Version2.0
Created at2022-09-07 07:56:27 UTC
Updated at2022-09-07 07:56:27 UTC
NP-MRD IDNP0246452
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,4,5-trihydroxy-3-methoxypentanal
Description2,4,5-Trihydroxy-3-methoxypentanal belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 2,4,5-trihydroxy-3-methoxypentanal is found in Myxococcus fulvus. 2,4,5-Trihydroxy-3-methoxypentanal is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)


  Mrv1533004161523232D          

 11 10  0  0  0  0            999 V2000
    4.6184    0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  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
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   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
    4.6184    2.6664    0.0000 O   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  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
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
Download

3D MOL for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)

     RDKit          3D

 23 22  0  0  0  0  0  0  0  0999 V2000
    0.1475    2.7713    0.2817 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3411    1.5139    0.8073 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1485    0.4861   -0.1552 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4243   -0.2270   -0.4081 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3628   -1.2438   -1.3518 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0839   -0.7706    0.7944 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2636   -0.0754    1.7791 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0377   -0.3434    0.2076 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9853   -0.9860    1.4178 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3968   -1.3738   -0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6477   -1.9436   -0.5816 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8905    2.8758   -0.1105 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7931    2.8225   -0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4815    3.5856    0.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1118    1.0429   -1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1242    0.5386   -0.8649 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7603   -2.0798   -1.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4311   -1.7943    0.8529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9667    0.3182    0.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3492   -0.4393    2.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3563   -0.9418   -1.8342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6316   -2.2049   -0.8133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9881   -1.5312    0.2331 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  6
  8 19  1  1
  9 20  1  0
 10 21  1  0
 10 22  1  0
 11 23  1  0
  4 16  1  6
  5 17  1  0
  6 18  1  0
M  END
Download

3D SDF for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)


  Mrv1533004161523232D          

 11 10  0  0  0  0            999 V2000
    4.6184    0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  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
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   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
    4.6184    2.6664    0.0000 O   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  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
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0246452

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(C(O)CO)C(O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-11-6(4(9)2-7)5(10)3-8/h2,4-6,8-10H,3H2,1H3

> <INCHI_KEY>
JNAZNWGFTWHNTH-UHFFFAOYSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.157

> <EXACT_MASS>
164.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.358714782443693

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,4,5-trihydroxy-3-methoxypentanal

> <ALOGPS_LOGP>
-1.64

> <JCHEM_LOGP>
-2.294899117333333

> <ALOGPS_LOGS>
0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.47349773798613

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.430119582422503

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974701900628598

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
36.134299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.83e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4,5-trihydroxy-3-methoxypentanal

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)

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PDB for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)
HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       8.621   0.357   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+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       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6                                                            
CONECT    8    3    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)
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SMILES for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)
COC(C(O)CO)C(O)C=O
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INCHI for NP0246452 (2,4,5-trihydroxy-3-methoxypentanal)
InChI=1S/C6H12O5/c1-11-6(4(9)2-7)5(10)3-8/h2,4-6,8-10H,3H2,1H3
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View in JSmol
Synonyms
ValueSource
3-O-MethylxyloseMeSH
3-MethylxyloseMeSH
3-O-Methyl-L-xyloseMeSH
Chemical FormulaC6H12O5
Average Mass164.1570 Da
Monoisotopic Mass164.06847 Da
IUPAC Name2,4,5-trihydroxy-3-methoxypentanal
Traditional Name2,4,5-trihydroxy-3-methoxypentanal
CAS Registry NumberNot Available
SMILES
COC(C(O)CO)C(O)C=O
InChI Identifier
InChI=1S/C6H12O5/c1-11-6(4(9)2-7)5(10)3-8/h2,4-6,8-10H,3H2,1H3
InChI KeyJNAZNWGFTWHNTH-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
Myxococcus fulvusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentPentoses  
Alternative Parents
Substituents
  • Pentose monosaccharide
    • 

  • Alpha-hydroxyaldehyde
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Ether
    • 

  • Dialkyl ether
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Aldehyde
    • 

  • 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-1.6ALOGPS
logP-2.3ChemAxon
logS0.47ALOGPS
pKa (Strongest Acidic)12.43ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.99 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity36.13 m³·mol⁻¹ChemAxon
Polarizability15.36 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound22271855  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]