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Showing NP-Card for 1,3-dihydroxypentane-1,3,5-tricarboxylic acid (NP0312138)

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Record Information
Version2.0
Created at2022-09-11 08:40:35 UTC
Updated at2022-09-11 08:40:35 UTC
NP-MRD IDNP0312138
Secondary Accession NumbersNone
Natural Product Identification
Common Name1,3-dihydroxypentane-1,3,5-tricarboxylic acid
Description1,3-Dihydroxypentane-1,3,5-tricarboxylic acid belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. 1,3-dihydroxypentane-1,3,5-tricarboxylic acid is found in Euphorbia palustris. 1,3-Dihydroxypentane-1,3,5-tricarboxylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)


  Mrv1533004161506542D          

 16 15  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    5.0013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
M  END
Download

3D MOL for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)

     RDKit          3D

 28 27  0  0  0  0  0  0  0  0999 V2000
   -3.6070    0.7928    1.4398 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3809    0.8282    0.2028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0510    1.8037   -0.5230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4424   -0.1309   -0.4334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0296    0.3774   -0.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0018   -0.5242   -0.7929 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1688   -0.4796   -2.2035 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3734    0.0230   -0.5405 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8314    0.0803    0.8660 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0944    0.8530    1.7343 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2471    0.5900    0.9335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5840    1.5462    1.6796 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2017   -0.0325    0.1342 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0796   -1.9142   -0.3626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2775   -2.8056   -1.2251 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0449   -2.3509    0.9452 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7430    2.7707   -0.4428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6393   -0.1571   -1.5046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5261   -1.0959    0.0888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9535    1.3640   -0.6832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9383    0.5408    0.8999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1460    0.4878   -2.4739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4319    1.0737   -0.9752 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1426   -0.5424   -1.1527 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9061   -0.9767    1.2643 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.4729    2.6534 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4489    0.3893   -0.7512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5604   -2.9836    1.4106 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  6  1  0
  6  7  1  6
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  6 14  1  0
 14 16  1  0
 14 15  2  0
  9 11  1  0
 11 13  1  0
 11 12  2  0
 10 26  1  0
  9 25  1  1
  8 23  1  0
  8 24  1  0
  7 22  1  0
  5 20  1  0
  5 21  1  0
  4 18  1  0
  4 19  1  0
  3 17  1  0
 16 28  1  0
 13 27  1  0
M  END
Download

3D SDF for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)


  Mrv1533004161506542D          

 16 15  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    5.0013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0312138

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(CC(O)(CCC(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H12O8/c9-4(6(12)13)3-8(16,7(14)15)2-1-5(10)11/h4,9,16H,1-3H2,(H,10,11)(H,12,13)(H,14,15)

> <INCHI_KEY>
CQBQTNMBPLCAHQ-UHFFFAOYSA-N

> <FORMULA>
C8H12O8

> <MOLECULAR_WEIGHT>
236.176

> <EXACT_MASS>
236.053217346

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.46295704467147

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-dihydroxypentane-1,3,5-tricarboxylic acid

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-1.6892249686666665

> <ALOGPS_LOGS>
-0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.5040241943378656

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8901677992051815

> <JCHEM_PKA_STRONGEST_BASIC>
-3.848108306800488

> <JCHEM_POLAR_SURFACE_AREA>
152.36

> <JCHEM_REFRACTIVITY>
46.58250000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.85e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-dihydroxypentane-1,3,5-tricarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)

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PDB for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)
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  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.644   3.231   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.080   5.335   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310   6.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.080   8.002   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.310   9.336   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.620   8.002   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.976   4.771   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.976   6.311   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.357   4.001   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6   11                                             
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    4   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    2   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

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3D PDB for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)
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SMILES for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)
OC(CC(O)(CCC(O)=O)C(O)=O)C(O)=O
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INCHI for NP0312138 (1,3-dihydroxypentane-1,3,5-tricarboxylic acid)
InChI=1S/C8H12O8/c9-4(6(12)13)3-8(16,7(14)15)2-1-5(10)11/h4,9,16H,1-3H2,(H,10,11)(H,12,13)(H,14,15)
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View in JSmol
Synonyms
ValueSource
1,3-Dihydroxypentane-1,3,5-tricarboxylateGenerator
Chemical FormulaC8H12O8
Average Mass236.1760 Da
Monoisotopic Mass236.05322 Da
IUPAC Name1,3-dihydroxypentane-1,3,5-tricarboxylic acid
Traditional Name1,3-dihydroxypentane-1,3,5-tricarboxylic acid
CAS Registry NumberNot Available
SMILES
OC(CC(O)(CCC(O)=O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C8H12O8/c9-4(6(12)13)3-8(16,7(14)15)2-1-5(10)11/h4,9,16H,1-3H2,(H,10,11)(H,12,13)(H,14,15)
InChI KeyCQBQTNMBPLCAHQ-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
Euphorbia palustrisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassTricarboxylic acids and derivatives  
Direct ParentTricarboxylic acids and derivatives  
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
    • 

  • Hydroxy acid
    • 

  • Alpha-hydroxy acid
    • 

  • Tertiary alcohol
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • 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-1.8ALOGPS
logP-1.7ChemAxon
logS-0.11ALOGPS
pKa (Strongest Acidic)2.89ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area152.36 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity46.58 m³·mol⁻¹ChemAxon
Polarizability20.46 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 CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]