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Showing NP-Card for 3-Deoxy-arabino-hexaric acid (NP0073307)

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Record Information
Version2.0
Created at2022-04-28 18:35:12 UTC
Updated at2022-04-28 18:35:13 UTC
NP-MRD IDNP0073307
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Deoxy-arabino-hexaric acid
Description(2S,3S,5S)-2,3,5-trihydroxyhexanedioic acid belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. 3-Deoxy-arabino-hexaric acid is found in Pycnandra acuminata and Sebertia acuminata. Based on a literature review very few articles have been published on (2S,3S,5S)-2,3,5-trihydroxyhexanedioic acid.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0073307 (3-Deoxy-arabino-hexaric acid)


  Mrv1652304282220352D          

 13 12  0  0  1  0            999 V2000
    3.9039    1.4289    0.0000 C   0  0  1  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
    2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 O   0  0  0  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
    4.6184    1.8414    0.0000 C   0  0  1  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
    5.3329    0.6039    0.0000 O   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
    3.9039    0.6039    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  2  0  0  0  0
  4  6  1  0  0  0  0
  3  7  1  6  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  6  0  0  0
  1 13  1  1  0  0  0
M  END
Download

3D MOL for NP0073307 (3-Deoxy-arabino-hexaric acid)

     RDKit          3D

 23 22  0  0  0  0  0  0  0  0999 V2000
    2.0081   -0.2871    1.6653 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1960    0.6055    0.8093 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4829    1.0802    0.6431 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0629    1.1055    0.0283 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5163    2.1068   -0.8644 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3951    0.0668   -0.8320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1594   -1.0871   -0.0859 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7527   -1.9623   -1.0111 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2046   -0.7426    0.9395 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6516   -1.8998    1.6074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3969   -0.0673    0.3930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5379   -0.5897    0.5285 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2497    1.1521   -0.2720 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9979    1.0438   -0.2225 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2950    1.6171    0.6553 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0134    1.6071   -1.5647 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1840   -0.2536   -1.5782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3703    0.5715   -1.4425 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6548   -1.6922    0.3861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0505   -1.4656   -1.8110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7348   -0.1161    1.7519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7617   -2.6569    1.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9361    1.8640   -0.1733 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 13  1  0
 11 12  2  0
  8 20  1  0
  7 19  1  1
  6 17  1  0
  6 18  1  0
  4 15  1  1
  5 16  1  0
  3 14  1  0
  9 21  1  1
 10 22  1  0
 13 23  1  0
M  END
Download

3D SDF for NP0073307 (3-Deoxy-arabino-hexaric acid)


  Mrv1652304282220352D          

 13 12  0  0  1  0            999 V2000
    3.9039    1.4289    0.0000 C   0  0  1  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
    2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 O   0  0  0  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
    4.6184    1.8414    0.0000 C   0  0  1  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
    5.3329    0.6039    0.0000 O   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
    3.9039    0.6039    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  2  0  0  0  0
  4  6  1  0  0  0  0
  3  7  1  6  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  6  0  0  0
  1 13  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0073307

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O7/c7-2(4(9)6(12)13)1-3(8)5(10)11/h2-4,7-9H,1H2,(H,10,11)(H,12,13)/t2-,3-,4-/m0/s1

> <INCHI_KEY>
WZLURCXZSPTANB-HZLVTQRSSA-N

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.139

> <EXACT_MASS>
194.042652662

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.493549551873617

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,5S)-2,3,5-trihydroxyhexanedioic acid

> <ALOGPS_LOGP>
-1.80

> <JCHEM_LOGP>
-2.3991750916666663

> <ALOGPS_LOGS>
-0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.681071367294181

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9560701212600518

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3049712396842983

> <JCHEM_POLAR_SURFACE_AREA>
135.29

> <JCHEM_REFRACTIVITY>
37.0413

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.62e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,5S)-2,3,5-trihydroxyhexanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0073307 (3-Deoxy-arabino-hexaric acid)

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PDB for NP0073307 (3-Deoxy-arabino-hexaric acid)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       3.286   4.977   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.620   1.127   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  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
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
CONECT    1    2    8   13                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
CONECT    8    1    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8                                                            
CONECT   13    1                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for NP0073307 (3-Deoxy-arabino-hexaric acid)
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SMILES for NP0073307 (3-Deoxy-arabino-hexaric acid)
O[C@@H](C[C@H](O)C(O)=O)[C@H](O)C(O)=O
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INCHI for NP0073307 (3-Deoxy-arabino-hexaric acid)
InChI=1S/C6H10O7/c7-2(4(9)6(12)13)1-3(8)5(10)11/h2-4,7-9H,1H2,(H,10,11)(H,12,13)/t2-,3-,4-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S,3S,5S)-2,3,5-TrihydroxyhexanedioateGenerator
Chemical FormulaC6H10O7
Average Mass194.1390 Da
Monoisotopic Mass194.04265 Da
IUPAC Name(2S,3S,5S)-2,3,5-trihydroxyhexanedioic acid
Traditional Name(2S,3S,5S)-2,3,5-trihydroxyhexanedioic acid
CAS Registry NumberNot Available
SMILES
O[C@@H](C[C@H](O)C(O)=O)[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H10O7/c7-2(4(9)6(12)13)1-3(8)5(10)11/h2-4,7-9H,1H2,(H,10,11)(H,12,13)/t2-,3-,4-/m0/s1
InChI KeyWZLURCXZSPTANB-HZLVTQRSSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Pycnandra acuminataLOTUS Database
Sebertia acuminataPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassHydroxy acids and derivatives  
Sub ClassMedium-chain hydroxy acids and derivatives  
Direct ParentMedium-chain hydroxy acids and derivatives  
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
    • 

  • Medium-chain fatty acid
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy fatty acid
    • 

  • Alpha-hydroxy acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Monosaccharide
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Polyol
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • 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-1.8ALOGPS
logP-2.4ChemAxon
logS-0.35ALOGPS
pKa (Strongest Acidic)2.96ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area135.29 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.04 m³·mol⁻¹ChemAxon
Polarizability16.49 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 ID75159385  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound92209640  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References