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Showing NP-Card for 2-Carboxyarabinitol (NP0049752)

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Record Information
Version2.0
Created at2022-03-17 21:17:34 UTC
Updated at2022-03-17 21:17:34 UTC
NP-MRD IDNP0049752
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Carboxyarabinitol
Description2-Carboxyarabinitol belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 2-Carboxyarabinitol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0049752 (2-Carboxyarabinitol)


  Mrv0541 02241215192D          

 13 12  0  0  0  0            999 V2000
    0.7424   -1.8156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -1.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5773   -1.8985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4031   -0.9898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8254   -0.4951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -0.5773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8254   -0.5773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6603    0.7424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    0.2477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    0.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4031    0.4121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    1.4853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    1.8985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
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3D MOL for NP0049752 (2-Carboxyarabinitol)

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3D SDF for NP0049752 (2-Carboxyarabinitol)

  Mrv0541 02241215192D          

 13 12  0  0  0  0            999 V2000
    0.7424   -1.8156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -1.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5773   -1.8985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4031   -0.9898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8254   -0.4951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -0.5773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8254   -0.5773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6603    0.7424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    0.2477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    0.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4031    0.4121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    1.4853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    1.8985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049752

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3-4,7-10,13H,1-2H2,(H,11,12)

> <INCHI_KEY>
XONDRGRALZTVKD-UHFFFAOYSA-N

> <FORMULA>
C6H12O7

> <MOLECULAR_WEIGHT>
196.1553

> <EXACT_MASS>
196.058302738

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.054962098445248

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid

> <ALOGPS_LOGP>
-2.44

> <JCHEM_LOGP>
-3.3935534493333335

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.082634557256219

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.304239008548323

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9748649602552684

> <JCHEM_POLAR_SURFACE_AREA>
138.45000000000002

> <JCHEM_REFRACTIVITY>
38.5655

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.57e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0049752 (2-Carboxyarabinitol)
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PDB for NP0049752 (2-Carboxyarabinitol)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       1.386  -3.389   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.001  -2.619   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.078  -3.544   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.619  -1.848   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.541  -0.924   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.001  -1.078   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.541  -1.078   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.233   1.386   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.001   0.462   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.233   1.233   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.619   0.769   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.233   2.773   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.001   3.544   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2                                                            
CONECT    4    5                                                            
CONECT    5    4    6                                                       
CONECT    6    2    5    7    9                                             
CONECT    7    6                                                            
CONECT    8    9                                                            
CONECT    9    6    8   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for NP0049752 (2-Carboxyarabinitol)
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SMILES for NP0049752 (2-Carboxyarabinitol)
OCC(O)C(O)C(O)(CO)C(O)=O
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INCHI for NP0049752 (2-Carboxyarabinitol)
InChI=1S/C6H12O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3-4,7-10,13H,1-2H2,(H,11,12)
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SynonymsNot Available
Chemical FormulaC6H12O7
Average Mass196.1553 Da
Monoisotopic Mass196.05830 Da
IUPAC Name2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid
Traditional Name2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(O)(CO)C(O)=O
InChI Identifier
InChI=1S/C6H12O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3-4,7-10,13H,1-2H2,(H,11,12)
InChI KeyXONDRGRALZTVKD-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Artemisia dracunculusFooDB
Avena sativa L.FooDB
Citrus limonFooDB
Ginkgo bilobaFooDB
Glycine maxFooDB
Hordeum vulgareFooDB
Mentha spicataFooDB
Phaseolus vulgarisFooDB
Spinacia oleraceaFooDB
Taraxacum officinaleFooDB
Zea mays L.FooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acids and conjugates  
Direct ParentHydroxy fatty acids  
Alternative Parents
Substituents
  • Beta-hydroxy acid
    • 

  • Branched fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Hydroxy fatty acid
    • 

  • Alpha-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • Tertiary alcohol
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Polyol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • 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-2.4ALOGPS
logP-3.4ChemAxon
logS0.52ALOGPS
pKa (Strongest Acidic)3.3ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area138.45 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity38.57 m³·mol⁻¹ChemAxon
Polarizability17.05 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB020764  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5165850  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available