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Showing NP-Card for 2,3,4-trihydroxypentanoic acid (NP0190813)

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Record Information
Version2.0
Created at2022-09-04 07:33:21 UTC
Updated at2022-09-04 07:33:21 UTC
NP-MRD IDNP0190813
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,3,4-trihydroxypentanoic acid
Description2,3,4-Trihydroxypentanoic acid belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 2,3,4-trihydroxypentanoic acid is found in Nymphaea caerulea. 2,3,4-Trihydroxypentanoic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0190813 (2,3,4-trihydroxypentanoic acid)


  Mrv1533004191514442D          

 10  9  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    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
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  2  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
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
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3D MOL for NP0190813 (2,3,4-trihydroxypentanoic acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.2417    0.0012    0.3551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2426   -0.2798   -0.7341 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5554   -1.5621   -1.2391 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1611   -0.3598   -0.2159 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2154   -1.3109    0.7725 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7085    0.9655    0.2350 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6394    1.8961   -0.7786 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1548    0.7428    0.5762 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0737    1.3414   -0.0093 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4720   -0.1639    1.5812 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8347    0.5684    1.2016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0677    0.6043   -0.1151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7609   -0.9361    0.7065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2708    0.4733   -1.5493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1543   -2.2347   -0.6399 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8055   -0.6852   -1.0826 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7143   -2.1227    0.4458 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2107    1.3440    1.1516 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0245    2.7495   -0.4034 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9480   -1.0314    1.4005 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8 10  1  0
  8  9  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  3 15  1  0
  4 16  1  6
  5 17  1  0
  6 18  1  1
  7 19  1  0
 10 20  1  0
M  END
Download

3D SDF for NP0190813 (2,3,4-trihydroxypentanoic acid)


  Mrv1533004191514442D          

 10  9  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    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
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  2  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
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0190813

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c1-2(6)3(7)4(8)5(9)10/h2-4,6-8H,1H3,(H,9,10)

> <INCHI_KEY>
CHUMGDDVFASTDV-UHFFFAOYSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.13

> <EXACT_MASS>
150.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.418734810414776

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4-trihydroxypentanoic acid

> <ALOGPS_LOGP>
-1.82

> <JCHEM_LOGP>
-1.7324994019999997

> <ALOGPS_LOGS>
0.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.932856615973709

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5716049726631343

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0563265174813417

> <JCHEM_POLAR_SURFACE_AREA>
97.99

> <JCHEM_REFRACTIVITY>
30.7648

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.68e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,4-trihydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0190813 (2,3,4-trihydroxypentanoic acid)

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PDB for NP0190813 (2,3,4-trihydroxypentanoic acid)
HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.977  -0.206   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    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0190813 (2,3,4-trihydroxypentanoic acid)
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SMILES for NP0190813 (2,3,4-trihydroxypentanoic acid)
CC(O)C(O)C(O)C(O)=O
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INCHI for NP0190813 (2,3,4-trihydroxypentanoic acid)
InChI=1S/C5H10O5/c1-2(6)3(7)4(8)5(9)10/h2-4,6-8H,1H3,(H,9,10)
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View in JSmol
Synonyms
ValueSource
2,3,4-TrihydroxypentanoateGenerator
5-Deoxy-ribonateGenerator
Chemical FormulaC5H10O5
Average Mass150.1300 Da
Monoisotopic Mass150.05282 Da
IUPAC Name2,3,4-trihydroxypentanoic acid
Traditional Name2,3,4-trihydroxypentanoic acid
CAS Registry NumberNot Available
SMILES
CC(O)C(O)C(O)C(O)=O
InChI Identifier
InChI=1S/C5H10O5/c1-2(6)3(7)4(8)5(9)10/h2-4,6-8H,1H3,(H,9,10)
InChI KeyCHUMGDDVFASTDV-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
Nymphaea caeruleaLOTUS Database
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
    • 

  • Hydroxy fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Methyl-branched fatty acid
    • 

  • Monosaccharide
    • 

  • Hydroxy acid
    • 

  • Alpha-hydroxy acid
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Polyol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen 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-1.8ALOGPS
logP-1.7ChemAxon
logS0.25ALOGPS
pKa (Strongest Acidic)3.57ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity30.76 m³·mol⁻¹ChemAxon
Polarizability13.42 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 Compound19930327  
PDB IDNot Available
ChEBI ID131364  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]