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Showing NP-Card for Pentaric acid (NP0084336)

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Record Information
Version2.0
Created at2022-04-29 05:05:52 UTC
Updated at2022-04-29 05:05:52 UTC
NP-MRD IDNP0084336
Secondary Accession NumbersNone
Natural Product Identification
Common NamePentaric acid
DescriptionPentaric acid, also known as pentarate, belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. Pentaric acid is found in Carica papaya . Pentaric acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0084336 (Pentaric acid)


  Mrv1533004181500242D          

 12 11  0  0  0  0            999 V2000
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  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
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    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  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
    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
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3D MOL for NP0084336 (Pentaric acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    3.0692    0.5877   -1.2257 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1798    0.5560   -0.3444 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8826    1.7427    0.2958 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4380   -0.6593    0.0506 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0553   -1.7060   -0.7003 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0204   -0.6384   -0.4693 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4615   -1.9521   -0.1992 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9143    0.2812    0.2222 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6688    1.6281    0.0850 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2790    0.0107   -0.3546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7107   -1.1695   -0.3338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0702    1.0080   -0.9032 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5155    2.0178    1.0486 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5201   -0.9145    1.1102 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6534   -1.7621   -1.6034 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0548   -0.4150   -1.5323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2944   -2.1155    0.7608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0076    0.0860    1.3135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0930    2.1236    0.8211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8896    1.2905   -0.3596 H   0  0  0  0  0  0  0  0  0  0  0  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
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 12  1  0
 10 11  2  0
  7 17  1  0
  6 16  1  6
  4 14  1  1
  5 15  1  0
  3 13  1  0
  8 18  1  1
  9 19  1  0
 12 20  1  0
M  END
Download

3D SDF for NP0084336 (Pentaric acid)


  Mrv1533004181500242D          

 12 11  0  0  0  0            999 V2000
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  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
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    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  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
    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084336

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O7/c6-1(2(7)4(9)10)3(8)5(11)12/h1-3,6-8H,(H,9,10)(H,11,12)

> <INCHI_KEY>
NPTTZSYLTYJCPR-UHFFFAOYSA-N

> <FORMULA>
C5H8O7

> <MOLECULAR_WEIGHT>
180.112

> <EXACT_MASS>
180.027002598

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.22190797613187

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.41

> <JCHEM_LOGP>
-2.4591348306666667

> <ALOGPS_LOGS>
-0.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.518885023851425

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.786220846412511

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8007073200227532

> <JCHEM_POLAR_SURFACE_AREA>
135.29

> <JCHEM_REFRACTIVITY>
32.1759

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.69e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0084336 (Pentaric acid)

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PDB for NP0084336 (Pentaric acid)
HEADER    PROTEIN                                 18-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-APR-15         0                                  
HETATM    1  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.286   3.437   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  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    2    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0084336 (Pentaric acid)
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SMILES for NP0084336 (Pentaric acid)
OC(C(O)C(O)=O)C(O)C(O)=O
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INCHI for NP0084336 (Pentaric acid)
InChI=1S/C5H8O7/c6-1(2(7)4(9)10)3(8)5(11)12/h1-3,6-8H,(H,9,10)(H,11,12)
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Synonyms
ValueSource
PentarateGenerator
2,3,4-TrihydroxypentanedioateGenerator
Chemical FormulaC5H8O7
Average Mass180.1120 Da
Monoisotopic Mass180.02700 Da
IUPAC Name2,3,4-trihydroxypentanedioic acid
Traditional Name2,3,4-trihydroxypentanedioic acid
CAS Registry NumberNot Available
SMILES
OC(C(O)C(O)=O)C(O)C(O)=O
InChI Identifier
InChI=1S/C5H8O7/c6-1(2(7)4(9)10)3(8)5(11)12/h1-3,6-8H,(H,9,10)(H,11,12)
InChI KeyNPTTZSYLTYJCPR-UHFFFAOYSA-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
Carica papaya L.Plant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassHydroxy acids and derivatives  
Sub ClassBeta hydroxy acids and derivatives  
Direct ParentBeta hydroxy acids and derivatives  
Alternative Parents
Substituents
  • Beta-hydroxy acid
    • 

  • Short-chain hydroxy acid
    • 

  • Alpha-hydroxy acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Monosaccharide
    • 

  • Fatty acid
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • 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-1.4ALOGPS
logP-2.5ChemAxon
logS-0.32ALOGPS
pKa (Strongest Acidic)2.79ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area135.29 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.18 m³·mol⁻¹ChemAxon
Polarizability14.22 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 Compound109475  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available