Showing NP-Card for 2-Keto-3-deoxy-D-gluconic acid (NP0086761)

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Record Information
Version2.0
Created at2022-05-11 16:30:15 UTC
Updated at2022-05-11 16:30:15 UTC
NP-MRD IDNP0086761
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Keto-3-deoxy-D-gluconic acid
Description2-Keto-3-deoxy-D-gluconic acid, also known as 2-dehydro-3-deoxy-D-galactonate or 3-deoxy-D-threo-hexulosonic acid, belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain. 2-Keto-3-deoxy-D-gluconic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 2-Keto-3-deoxy-D-gluconic acid exists in all living organisms, ranging from bacteria to humans. The 2-dehydro-3-deoxy derivative of D-galactonic acid.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)

  Mrv0541 02231219052D          

 12 11  0  0  1  0            999 V2000
    2.7165   -4.7233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8599   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5744   -4.7233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5744   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2888   -4.3108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2888   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0033   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7177   -4.3108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  6  0  0  0
  9  7  1  0  0  0  0
  9 10  1  6  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
M  END
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3D MOL for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)

     RDKit          3D

 22 21  0  0  0  0  0  0  0  0999 V2000
    3.1596   -1.1572    0.9389 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1731   -0.0768    0.2753 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3941    0.2987   -0.2512 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9739    0.7229    0.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0728    1.7780   -0.5921 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6682    0.3097    0.6476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1622   -0.2297   -0.4700 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4966   -1.2337   -1.1802 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5154   -0.6954   -0.0818 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2728   -1.0118   -1.2063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2979    0.2475    0.7603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5938    1.4164    0.0653 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7258    1.2434   -0.1939 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1441    1.2409    1.0142 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8748   -0.3984    1.4576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2870    0.6183   -1.2065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6460   -1.9881   -0.5564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4238   -1.6691    0.4840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2406   -0.8675   -0.9945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8441    0.4543    1.7514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2745   -0.2458    0.9937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4169    1.2433   -0.4610 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11  9  1  0
  9 10  1  0
  9  7  1  0
  7  8  1  0
  7  6  1  0
  6  4  1  0
  4  5  2  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 12 22  1  0
 11 20  1  0
 11 21  1  0
  9 18  1  1
 10 19  1  0
  7 16  1  6
  8 17  1  0
  6 14  1  0
  6 15  1  0
  3 13  1  0
M  END
Download

3D SDF for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)

  Mrv0541 02231219052D          

 12 11  0  0  1  0            999 V2000
    2.7165   -4.7233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8599   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5744   -4.7233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5744   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2888   -4.3108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2888   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0033   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7177   -4.3108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  6  0  0  0
  9  7  1  0  0  0  0
  9 10  1  6  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086761

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1

> <INCHI_KEY>
WPAMZTWLKIDIOP-NQXXGFSBSA-N

> <FORMULA>
C6H10O6

> <MOLECULAR_WEIGHT>
178.14

> <EXACT_MASS>
178.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
15.535652108876848

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

> <ALOGPS_LOGP>
-1.87

> <JCHEM_LOGP>
-1.7750312403333335

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.243645462336318

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9051234753891952

> <JCHEM_PKA_STRONGEST_BASIC>
-2.972361954381558

> <JCHEM_POLAR_SURFACE_AREA>
115.06

> <JCHEM_REFRACTIVITY>
36.3163

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.34e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)

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PDB for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       5.071  -8.817   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.405  -8.047   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       6.405  -6.507   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       7.738  -8.817   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.738 -10.357   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       9.072  -8.047   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.406  -8.817   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      10.406 -10.357   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      11.739  -8.047   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.739  -6.507   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.073  -8.817   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      14.406  -8.047   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                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)
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SMILES for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)
OC[C@@H](O)[C@H](O)CC(=O)C(O)=O
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INCHI for NP0086761 (2-Keto-3-deoxy-D-gluconic acid)
InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1
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View in JSmol
Synonyms
ValueSource
2-Dehydro-3-deoxy-D-galactonateChEBI
2-Dehydro-3-deoxy-D-galactonic acidGenerator
2-Keto-3-deoxy-D-gluconateGenerator
2-oxo-3-Deoxygalactonic acidHMDB
3-Deoxy-D-threo-hexulosonic acidHMDB
Chemical FormulaC6H10O6
Average Mass178.1400 Da
Monoisotopic Mass178.04774 Da
IUPAC Name(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid
Traditional Name(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)[C@H](O)CC(=O)C(O)=O
InChI Identifier
InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1
InChI KeyWPAMZTWLKIDIOP-NQXXGFSBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12  carbon atoms long side chain.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassKeto acids and derivatives  
Sub ClassMedium-chain keto acids and derivatives  
Direct ParentMedium-chain keto acids and derivatives  
Alternative Parents
Substituents
  • Medium-chain keto acid
    • 

  • Alpha-keto acid
    • 

  • Beta-hydroxy ketone
    • 

  • Alpha-hydroxy ketone
    • 

  • Secondary alcohol
    • 

  • Ketone
    • 

  • Polyol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • 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-1.9ALOGPS
logP-1.8ChemAxon
logS-0.12ALOGPS
pKa (Strongest Acidic)2.91ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area115.06 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity36.32 m³·mol⁻¹ChemAxon
Polarizability15.54 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001353  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022572  
KNApSAcK IDNot Available
Chemspider ID168361  
KEGG Compound IDC01216  
BioCyc ID2-DEHYDRO-3-DEOXY-D-GLUCONATE  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6184  
PubChem Compound194024  
PDB IDNot Available
ChEBI ID17028  
Good Scents IDNot Available
References
General ReferencesNot Available